Currents provides an overview of issues that impact watersheds and fish in northern California. The opinions expressed in the articles below are those of the authors and may or may not reflect the positions of the BCWC.






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“Floodplain Fatties:” A Promising Start for Salmon

Tom Philp, Executive Strategist, Metropolitan Water District

Quintupling your weight in six weeks is generally not sound medical advice. Unless, that is, you happen to be a very young Northern California salmon trying to add a few grams on your way down river to the Pacific Ocean.

Back in October, I mentioned a pilot project Metropolitan was helping to fund that was to take place this winter. The idea was to learn more about the potential benefits of increasing the time juvenile salmon can spend on a healthy floodplain. The laboratory was the Yolo Bypass between the cities of Davis and Sacramento.

Five acres of a stubbled rice field were flooded. On Jan. 31, approximately 10,000 hatchery Chinook salmon were trucked to the bypass and carefully placed into the murky water.

They weighed barely more than a gram on average at the time.

Researchers from UC Davis and the California Department of Water Resources, among others, monitored the field. On March 12, a gate at a corner of the rice field was opened to drain the water with the salmon into a canal that reaches the Sacramento-San Joaquin Delta, the pathway to the Pacific. But before the gate was opened, researchers captured a sampling of salmon to weigh and measure before their journey toward the Delta and beyond.

The average weight – 5.27 grams.

The official conclusion: The salmon were “floodplain fatties.”

This is good news. Here is a recent presentation with more information. At the moment, salmon spill into the Yolo Bypass from the Sacramento River only when water levels are rather high. Long-range planning is under way to explore how to modify the connection between the river and the Yolo Bypass in order to direct more salmon, more frequently, onto the floodplain. The challenge is to do so in a manner that minimizes the impacts to agricultural activities such as rice farming, which clearly creates a diet-rich floodplain that the salmon enjoy. The bypass is one of those special landscapes with multiple values, from flood protection to agriculture to prime waterfowl habitat along the Pacific Flyway.

A larger, more elaborate pilot project is scheduled next winter to study more salmon on more acres. There is reason to hope that the Yolo Bypass can successfully grow rice in the summer and salmon in the winter.


New study underway on how to increase survival of juvenile salmon

Central Valley Business Times
May 16, 2012

California’s Department of Fish and Game says its biologists are trying a new tactic to help California’s ocean-bound juvenile salmon, in hopes of increasing survival rates.

On May 3, for the first time in state history, DFG staff used a boat to move approximately 100,000 young Chinook (called smolts) down the Sacramento River to San Francisco Bay. Upon arrival, the smolts were released in the Bay, where they will grow to adulthood before returning upriver to spawn.

“We’ve been using trucks to transport smolts to points downstream for years, but we’ve never moved them by barge, and we’ve never moved them this far,” says DFG Environmental Scientist Colin Purdy, who supervised the boat transport to the Bay Area. “Truck releases are typically much further upstream, and though they do shorten the fish’s journey to the ocean, they still face all kinds of hazards in the river.”

Salmon return to their spawning grounds using their sense of smell. The process, called imprinting, begins before birth as waters flow over the eggs and continues as they grow and make their way to the ocean. Each segment of water on their journey has distinctive chemical cues that they can re-trace to their spawning grounds.

Sacramento River water is circulated through pumps into the boat’s holding tank, where the fish are kept. The hope is that this may improve their ability to find their way back as an adult and predators are unable to access the fish in the holding tank during the journey downstream, the department says.

This is the beginning of a multi-year study program aimed at increasing return rates of salmon from the sea to their native rivers, says DFG.

Over the next few years, scientists will use the data collected from the fish to test and evaluate the idea that overall survival rates and increased adult returns can be better achieved by giving the young salmon a ride downstream.

To form a basis of comparison for this study, two other control groups of 100,000 smolts each were released by trucks in other locations at the same time as the barge release — one at a different location in the Bay, and one into the Sacramento River near Sacramento.

All 300,000 fish in this study were implanted with coded wire tags smaller than a tiny piece of pencil lead, which will ultimately enable scientists to tell which of the three groups the returning fish came from — the barge release, or one of the two truck releases.

The study is being conducted by DFG fisheries biologists with the support of the Commercial Salmon Trollers Advisory Committee, which donated the use of the boat, fuel and crew time to help ensure a successful start to the study. They have committed to helping DFG for the next three years of data collection.

“This has been a major cooperative effort and we really appreciate DFG’s willingness to work with everybody and look at new ways of doing things,” says Zeke Grader, executive director of the Pacific Coast Federation of Fishermen.


60,000 tiny salmon trucked to Pillar Point Harbor

By Aaron Kinney
San Mateo County Times
May 11, 2012

Aside from a traffic jam on Interstate 880, the salmon did not encounter any obstacles on their way to the sea.

After a four-hour drive Thursday in a 2,800-gallon steel tank, 60,000 tiny fish shot through 40 feet of vinyl hose Thursday into a pen floating off Johnson Pier in Pillar Point Harbor, just north of Half Moon Bay. They splashed and skittered on the surface for a few minutes before settling into deeper water.

Every year the California Department of Fish and Game trucks millions of hatchery-raised salmon to drop-off points in San Pablo Bay or the Delta. Thursday, however, was the first time they've been delivered to San Mateo County, now home to one of only two such pens on the California coast.

The finger-length salmon smolts from the Feather River Fish Hatchery in Oroville will spend two weeks acclimating to the temperature and salinity of the water in the mesh-enclosed pen before they are released into the Pacific Ocean. In a couple years, they'll return as adults to spawn or wind up on Bay Area dinner plates, said Kevin Shaffer, who oversees salmon and steelhead trout conservation for Fish and Game.

"We want these fish to do one of two things: end up being caught by fishermen or head back up to the Central Valley," Shaffer said.

The coastal pens are meant to give a small but measurable boost to the region's beleaguered Chinook salmon. The popular fish must run a gauntlet of man-made impediments on their way through the delta -- silt and pollution, pumps that divert water to Central Valley farmers, and river banks that have been stripped of protective vegetation. Studies show that salmon that circumvent those threats have a higher rate of survival.

"We're hoping to a play a role in the health of the fishery," said Marc Gorelnik, a director of the Coastside Fishing Club, a regional association of recreational fishermen that paid for the pen at Johnson Pier. "This by itself is not going to solve any problems."

In three weeks the club expects to get 120,000 more smolts from the Feather River hatchery. Next year it hopes to get as many as 480,000. If just 5 percent of those fish stick around the coast rather than return to the delta, that's 24,000 more fish that will be available for commercial and recreation trollers.

The project at Pillar Point is a collaboration between the fishing club, Fish and Game, and the Commercial Salmon Stamp Committee, which collects dues from salmon fishermen to pay for restoration projects. Gorelnik estimated the club has spent about $80,000 on two pens, only one of which is currently in use, while Fish and Game is bearing the cost of raising and transporting the salmon.

The 48-by-24-foot pens are equipped with solar-powered food dispensers and a second layer of netting to thwart potential predators, such as the sea lion that loitered a few feet away Thursday as the smolts were pumped into the enclosure. Seal and sea lion predation forced the Monterey Bay Salmon and Trout Project to abandon pens in Moss Landing and Monterey not long ago and move its operation to Santa Cruz.

"The pinnipeds just ran us out of there," said Bob Anderson, a director of the project, which claims to have had success in boosting the number of salmon available to local fishermen.

California's fall-run Chinook are bouncing back after the population collapsed in 2009 and 2010, but their position remains precarious. State hatcheries bolster the population by releasing roughly 30 million Chinook smolts a year, and fishery managers are exploring new ways to help the salmon.

Last week Pillar Point fisherman Mike McHenry picked up 100,000 smolts from the Feather River hatchery and brought them by boat to Fort Baker just east of the Golden Gate Bridge. Biologists want to determine whether fish transported by boat, with river water circulating through their holding tanks, have a higher rate of return to their spawning grounds than those moved by truck. They theorize that the salmon's sense of smell helps them recognize the rivers from which they originate.

The Pillar Point smolts, as well as those McHenry dropped off at the Golden Gate and another 100,000 that were brought there by truck, have been implanted with identifying markers known as coded-wire tags. When caught, the fish will be analyzed to calculate how many of each group survived and what percentage found their way back to the delta.


Steelhead trout lose out when water is low in wine country

By Sarah Yang
UC Berkeley News Center
May 7, 2012

BERKELEY — The competition between farmers and fish for precious water in California is intensifying in wine country, suggests a new study by biologists at the University of California, Berkeley.

The findings, published in the May issue of the journal Transactions of the American Fisheries Society, link higher death rates for threatened juvenile steelhead trout with low water levels in the summer and the amount of vineyard acreage upstream.

The researchers found that juvenile steelhead trout are particularly at risk during the dry summer season typical of California’s Mediterranean climate. Of the juvenile steelhead trout present in June, on average only 30 percent survived to the late summer. In years with higher rainfall and in watersheds with less vineyard land use, the survival of juvenile trout over the summer was significantly higher.

The researchers pointed out that summer stream flow has been inadequately addressed in salmon and trout conservation efforts. Previous studies have highlighted other limiting factors such as habitat degradation and water quality, but here researchers documented the importance of water quantity for restoring threatened populations.

“Nearly all of California’s salmon and trout populations are on the path to extinction and if we’re going to bring these fish back to healthy levels, we have to change the way we manage our water,” said lead author Theodore Grantham, a recent Ph.D. graduate from UC Berkeley’s Department of Environmental Science, Policy and Management (ESPM). “Water withdrawals for agricultural uses can reduce or eliminate the limited amount of habitat available to sustain these cold-water fish through the summer. I don’t suggest we get rid of vineyards, but we do need to focus our attention on water management strategies that reduce summer water use. I believe we can protect flows for fish and still have our glass of wine.”

Steelhead trout (Oncorhynchus mykiss), historically found throughout the North Pacific Ocean, are an ocean-going, or anadromous, form of rainbow trout of the salmon family. Like salmon, steelhead trout migrate from freshwater streams to the ocean before returning to their birthplace to spawn. Steelhead trout in Southern California and the upper Columbia River are endangered, and several other populations, including those in Northern California, are threatened.

While drought conditions clearly have an impact on water levels in streams, the study authors highlighted the role played by regional agriculture. Previous studies in Sonoma County have shown that stream flow drops when pumps draw water for vineyards. In addition to using water for irrigation, Grantham noted that farmers often pump water from streams to protect vines when freezing temperatures occur in the spring. Overhead sprinklers coat vines in a layer of water that quickly freezes to create a thermal barrier, preventing damage to the vines.

“Because frost threatens all of the region’s vineyards at the same time, there can be an incredible peak demand for water during a concentrated two to three days,” said Grantham, who is now a postdoctoral researcher at the Center for Watershed Sciences at UC Davis. “During a bad frost year, as much water could be used in just two weeks during the spring as in an entire season for standard irrigation needs.”

One possible solution, Grantham noted, is establishing small off-stream reservoirs to store water during times of high rainfall. Vineyards would be able to draw from these water stores during low-flow periods rather than directly from streams.

The new analysis is based upon nine years of fish count data taken from nine streams in Sonoma County, allowing researchers to account for year-to-year variability in precipitation and differences in land use.

The researchers acknowledged that there are many environmental factors that influence populations of salmon and steelhead trout, including ocean conditions, fisheries and habitat degradation, so isolating which factors are causing problems, and to what extent, is extremely difficult.

“This is the first scientific publication on how vineyards and summer stream flows relate to fish survivorship in California’s tributary streams,” said study principal investigator Adina Merenlender, cooperative extension specialist in ESPM. “It is the closest we have to substantiating claims by resource agencies and environmental organizations that juvenile salmon are being impacted by low flows during the summer and survive better with more flow. These findings will help inform an important environmental issue in California that is disturbing to conservationists and grape growers alike.”

Other co-authors of the study are David Newburn, now an assistant professor at the University of Maryland’s Department of Agricultural and Resource Economics, and Michael McCarthy, a research fellow at the University of Melbourne’s School of Botany.

The Environmental Protection Agency and the National Science Foundation helped support this research.


Herbicide regulations tighten over salmon protection

National Fisheries Service
April 13, 2012

A new draft biological opinion issued by the National Marine Fisheries Service has found that three commonly used herbicides are increasing the chance of extinction for threatened and endangered Pacific salmon and steelhead runs.

The assessment by the federal fisheries service reverses earlier assurances from the U.S. Environmental Protection Agency that the three poisons were "not likely to adversely affect" these dwindling salmon populations.

The biological opinion prescribes measures to keep oryzalin, pendamethalin, and trifluralin out of salmon waters in Washington, Oregon, California, and Idaho. It is the fifth such plan issued under a court settlement with fishermen and conservationists.

The new protections, which must be implemented within one year of a final Biological Opinion, include:

• Prohibiting aerial applications of the pesticides within 300 feet of salmon waters.

• Mandating a 10 foot vegetated strip or a 20-foot no spray zone between salmon waters and places where these herbicides are applied.

• Mandatory reporting of fish kills near where these chemicals were applied.

"This is a huge step forward for the health of our rivers," said Aimee Code Environmental Health Associate at the Northwest Center for Alternatives to Pesticides. "These findings are a reminder that chemical pest control comes at a high cost. The true solution is to expand the use of non-chemical solutions."

The 780 page assessment concluded that if these pesticides are used as currently authorized, they are "likely to jeopardize the continued existence" of threatened and endangered salmon and steelhead populations.

"The federal government has just acknowledged that these three chemicals are washing off into our rivers and streams and harming west coast salmon runs and who knows what else," said Steve Mashuda, of Earthjustice. "It is time for the government to stand up to pesticide industry and impose these much needed restrictions," he concluded.

Fishermen are pleased by the proposed measures designed to help restore struggling salmon runs. "These pesticides are poisons and do not belong in salmon streams," commented Glen Spain of the Pacific Coast Federation of Fishermen's Associations (PCFFA), a commercial fishing industry group.

"The bottom line of us is that poisoning salmon rivers puts our people out of work as well as creates a public health hazard. It is far more cost effective to keep these poisons out of our rivers to begin with than to try to clean up messes afterwards."

The three active ingredients are registered for uses both in agriculture and in urban areas. All three can be used in lawns and landscaping. Each herbicide is registered for weed control in a variety of crops. Some of the crops listed where these chemicals can be used include Christmas trees, vineyards, onions, potatoes, and dry beans.

They are also all registered for use along rights-of-way. This latest assessment was completed as part of an ongoing effort to address the harms from numerous pesticides. It was preceded by several years of legal wrangling by the Northwest Center for Alternatives to Pesticides, Pacific Coast Federation of Fishermen's Associations, with representation from Earthjustice.

This effort began in January 2001, when some of the groups first went to court to force EPA to protect salmon in the Pacific Northwest from 54 pesticides that EPA approved for use without checking with federal fish biologists, as required by the Endangered Species Act. As a result of that lawsuit, a federal court ordered EPA to consult with federal fish biologists at NMFS on the impacts these pesticides have on salmon and steelhead in the Pacific Northwest and California.

In 2007, NMFS settled a second lawsuit and agreed to complete the long overdue assessments over a four-year period.


Restoration pact offers Klamath Basin hope

Erik Bergren/
For the Times-Standard
April 12, 2012

Over 10,000 waterfowl have died in the Lower Klamath and Tule Lake National Wildlife Refuges in the last couple of weeks due to an avian cholera outbreak exacerbated by low water conditions. This is one of the largest drought-related die-offs the refuges have seen in their 100-year history.

During years of low precipitation, water allocations in the Klamath Basin are stretched. The refuges are dependent on water deliveries from the Bureau of Reclamation's Klamath Project and it can be difficult to balance water needs among fisheries, wildlife refuges, tribes and irrigators.

While not a perfect solution, implementation of the Klamath Basin Restoration Agreement would help Klamath basin wildlife refuges by allowing refuge managers flexibility in allocating a set amount of water to support spring and fall waterfowl migrations. Refuges would be on equal footing with irrigation deliveries for the first time.

The agreement represents local, community derived solutions to the Klamath Basin's water needs. If the agreement had been implemented, the magnitude of disease outbreak on the refuges would have been lessened because more flooded habitat would have been present. Currently, it is the only viable option to ensuring more reliable water deliveries to the refuge over the long term.

With the struggle to balance water between farms and fish, the refuges are often overlooked. Of all the wetlands within the Pacific Flyway, no area provides more important staging

habitats, both in the fall and spring, for migratory waterfowl than the marshes and lakes of the Klamath Basin. This spring, the refuge has been one of the driest on record. According to refuge managers, only 50 percent of the wetlands on the refuge contain water. That is 15,000 acres of wetlands flooded out of about 31,000 acres on the Lower Klamath refuge.

Legislation authorizing the Klamath Basin Restoration Agreement is now before Congress and is an example of a locally developed plan that would solve many of the water-balancing issues that these communities face after dry winters like the one we just experienced. It is time for Congress to act.


Mercury in fish at area lakes raises alarm; new regulations sought for Shasta, Whiskeytown


California Fall Run Chinook Looks Big For 2012

Sierra2thesea
March 3, 2012

The fall Chinook salmon runs on the US West Coast look good this year with the Klamath river run estimated at 1,567,000 fish, a 31 year old record. Returns of 3-year-old adults on the Klamath were only 21,000 in 2009.

The 2012 fall run estimate on the Sacramento River is 819,400, four times the number that returned in 2011.

Thank improving ocean conditions, cold ocean water temps, that have nurtured growing salmon off the West Coast for the past few years after several disastrous years.

In February, the Pacific Fishery Management Council (PFMC) releases their Pacific salmon abundance estimates from the previous year to compare with their preseason forecasts and help develop management decisions for the season coming.

In 2011 the PFMC estimate for the Sacramento was 729,900 fish but the actual fish count came in far lower at 122,000, still much better than several years back when fears of a full blown fishery collapse hit the media. Back then,warmer ocean conditions in 2005 and 2006 led to a limited food supply as young salmon were entering the ocean resulting in low spawning returns in 2007 and 2008.

Rather than factor ocean conditions, a number of environmental critics charged California ag water users were to blame. But for the past several years the fishery has come back even as habitat has been restored.

Regarding the 2011 numbers,why the lower number from estimates? Were the fish harvested at sea or inland? The preliminary estimate of the harvest was 180,000 salmon in 2011 putting the total fish population ready to return up the Sacramento last year at 302,000 adding in the 122,000 who did return.

These expert estimates are educated guesses since Chinook salmon spend 1 to 8 years in the ocean - averaging from 3 to 4 years - before returning to their home rivers to spawn.

Get Back Jack
Scientists predict adult fish returns largely based on the pre-adult “jack” returns the year before although they are now weighing other factors.

The 2011 jacks about tripled the 2010 numbers,when they began to rise again - rebounding from their lows between 2007 to 2009. In 2007, only 2100 hatchery and wild jacks were counted. A total of 85,719 fall chinook jacks were estimated to have escaped to Sacramento River basin hatcheries and natural spawning areas in 2011. The PFMC has downplayed their previous reliance on jack estimates to some degree this year. If they relied on the formula used before, this years Sacramento fall run estimate would be 2.2 million instead of a more conservative 819,000.

In 2002, more than 800,000 fall Chinook salmon returned to the Sacramento River system, the most recent big year.

In the Klamath Basin, 2011 fall chinook jacks added up to 74,223 fish, with nearly 63,000 counted in natural spawning areas -the highest jack return since 1978 for the Klamath.

Of course, even if ocean conditions are good, this years fall river return might be problematic if it were solely based on the pitiful amount of rain and snow the state has received so far this season.

Dam Thankful
Ironically,critics of dams who say that these storage facilities reduce chances for returning fish survival may have to take a deep gulp and thank those same dams for retaining last years precipitation - carrying it over for 2012. This “savings account” of water stored benefits not just farms and cities this year,but returning salmon this fall. Dams like Shasta help keep water temps in the river cold enough to encourage survival of the fish in the 100 degree summer weather. A study released a few days ago found that raising the Shasta Dam 18.5 feet would increase the storage capacity of the lake by 14 percent improving both hydropower and salmon habitat.


A Bold Plan to Reshape the Central Valley Flood Plain

Overhaul aimed at preventing devastating floods and restoring habitats would cost tens of billions and sink farmland under water

By John Upton
The Bay Citizen
March 1, 2012

Jacob Katz stood shin-deep in a flooded rice paddy that is often dried out at this time of year. He thrust his hand into a writhing mass of baby salmon in his net and plucked three of the silver fry from the wind-whipped water’s surface.

In late January, five acres of this farmland in Yolo County was flooded and stocked with thousands of weeks-old Chinook salmon. It was the beginning of a three-year experiment that conservationists and government officials hope will provide scientific data to help guide a sweeping transformation of riverfront lands throughout the Central Valley, California’s prolific farming region.

“They were about two-thirds this size when we put them in,” said Katz, a doctoral candidate at the University of California, Davis, as the plump fry flapped off his palm and into the water. “They’re growing very, very rapidly. They’re looking great. It’s exactly what we want to see.”

An ambitious draft flood-prevention plan, published in December by the California Department of Water Resources, would re-engineer the valley’s network of rivers, canals and levees in an effort to prevent floods, restore wildlife habitat and protect water supplies for millions of people in the Bay Area and other parts of California. The plan, which calls for reversing the effects of 160 years of ad hoc levee building in the Central Valley, is a response to the deadly 2005 floods in New Orleans that followed Hurricane Katrina. Experts say a collapse of the Central Valley levees could cause similar devastation in California.
Yet the plan would take decades and cost tens of billions of dollars in local, state and federal money. It could also sink tens of thousands of acres of agricultural land under water, including parts of the Knaggs Ranch rice farm, where the baby salmon are growing along the Sacramento River.

Some farmers are angry because the plan, they said, enhances the environment and protects urban dwellers from floods at the expense of agricultural jobs and the rural economy. They also criticized state planners for failing to identify which parcels of land would be affected.

Jay Punia, executive officer of the Central Valley Flood Protection Board, which is charged with reviewing and approving the plan by July 1, said information about affected lands and other details about habitat restoration strategies sought by environmentalists would come after the draft is approved.

“This plan is basically a blueprint, a very high-level conceptual plan,” Punia said.
The baby fish in Katz’s net had spent three weeks in the experimental flood plain feasting on plankton and insects that young salmon historically relied upon to build their strength before venturing down rivers, through San Francisco Bay and into the Pacific Ocean.
Such nursery-style flood-plain habitats have nearly disappeared from the Central Valley. The creeks and rivers that carry rainwater and snowmelt from the Sierra Nevada and into the West Coast’s largest estuary were tamed long ago, lined with earthen levees that protect farms and a growing number of neighborhoods from the widespread flooding that defined the region until the middle of the 19th century.

Salmon, steelhead trout, Sacramento splittail and other native fish are not the only wildlife that flourish in the few remaining Central Valley flood plains. The habitats provide breeding, resting and feeding places for birds, including those that migrate along the heavily traveled avian highway between Mexico and Alaska, colloquially dubbed the Pacific Flyway.

Most of the levees, built as mounds of silt, sand and other materials found close to the riverbank, are in danger of collapsing. The Central Valley’s flood risks are considered among the most acute in the nation.

Such disasters could jeopardize $70 billion worth of property and infrastructure, put a million people at risk and contaminate or sever much of the state’s water supply, the Department of Water Resources estimates. Floods in 1983, 1986, 1995 and 1997 caused hundreds of thousands of people to be evacuated from their homes and resulted in more than $3 billion damage.

Until levee construction began in 1850, winter rains and melting snow would frequently cause rivers in the Central Valley to overflow. Shallow floodwaters teeming with wildlife would engulf the valley, flushing south and west until converging at the delta of the Sacramento and San Joaquin Rivers near Antioch, before gushing down into Suisun, San Pablo and San Francisco Bays.

Now, the more than 1,500 miles of levees confine most young salmon to river channels, where they are preyed upon as they grow by larger fish, including invasive striped bass, and are forced to battle currents as they hunt for midges, zooplankton and other food that was easier to find in the long-lost flood plains.

“There’s more to eat on a flood plain than there is in a river,” Katz said. “It’s warmer, and that’s better for the metabolism of salmon.”

The loss of spawning and flood-plain habitats has contributed to a near-collapse of salmon in the region. Hatchery-raised fish now dominate and sustain many of the salmon populations, but those fish have been found to have genetic weaknesses and other ailments that can exacerbate the species’ woes.

The experimental site is part of the Yolo Bypass, a managed plain that floods after winter storms douse the northern part of the state on an average of six years out of every 10. Researchers plan to spend three winters measuring how different approaches to managing the creek-front lands affect salmon growth rates.

The Yolo Bypass flood plain overlaps private and public land, including rice fields, duck hunting clubs and protected habitat. It works as a relief valve, absorbing water in wet years, preventing that water from knocking down or cascading over levees and rushing into populated areas.

Under the draft Central Valley Flood Protection Plan, and also under the department’s draft Bay Delta Conservation Plan, which seeks to balance economic and environmental uses of water, the flood plain would be expanded and could flood every year. Other flood plains would be created or expanded throughout the region to help restore riverside habitats and reduce flood risks. In some cases, levees would be set back farther from rivers, creating flood buffers and shallow flood-plain-style habitat.

The proposed overhaul would cause the loss of 10,000 acres of farmland, according to preliminary estimates. An additional 30,000 acres would be frequently inundated.
If they expand the Yolo Bypass, “it’s going to bring all my ground inside the bypass,” said Tim Miramontes, a farmer who grows rice and other crops on 1,500 acres of land that he leases near Knaggs Ranch. “Potentially, I could lose all of it.”

Sen. Lois Wolk, Democrat of Davis, one of the authors of the 2007 legislation that led to the flood planning process, acknowledged that the plan would be expensive and painful to put into action. But she said the risks of doing nothing could be far worse.

“It is a dramatic plan,” Wolk said. “The state taxpayer is liable for any damage that occurs if we haven’t fixed the levees. Not only is the taxpayer’s pocketbook at risk, but the cost in lives and disruption would be dramatic — worse, much worse, than Katrina.”


Fisheries officials face hostile crowd: Salmon recovery plan seen as flawed


Project aims to photograph every inch of Sacramento River

By Matt Weiser
Sacramento Bee
February 28, 2012

The Sacramento River this summer is set to become the first water body in the world to be documented inch-for-inch in photographs.

The goal of the Riverview Project is to apply to waterways the same techniques popularized by Google Street View. The popular Internet tool attaches 360-degree images to map locations, allowing a quick look at intersections, storefronts and front yards.

In the same way, an armchair traveler could use an online map to pick any point along the Sacramento River and view panoramic images of that location in all its gritty detail.

Jared Criscuolo, co-founder and executive director of the project, said the group also intends to attach environmental data to the maps and images, such as water quality and fisheries information.

"On one level, it's a basic exploration tool just to get people on the river," he said. "But on another level, this is a way to put together some really robust and unbiased information to help better protect not just the Sacramento River, but that vital source of water to keep the state as productive as it is."

The U.S. Geological Survey has taken an interest in the project, offering to help integrate its own data from existing water-quality monitors in the river. It may also provide boats, fuel and other tangible support, though spokeswoman Laurel Lynn Rogers said those details are yet to be firmed up.

"The collaboration is potentially of great value to the public as a way to provide more information about our nation's streams and waterways," Rogers said. "This may be another way for us to collect important visual information, and is potentially a way for more people to access our data in a user-friendly way."

Other partners include the Clif Bar Family Foundation and the Nature Conservancy. The Surfrider Foundation is serving as a financial custodian while the Riverview Project pursues nonprofit status of its own.

The finished project – complete with online maps, photos and integrated data – is expected to cost about $320,000, Criscuolo said. The public may make tax- deductible donations at http://riverviewproject.org/.

He said the group hopes to begin documenting the river in June or July, at the headwaters near the small city of Mount Shasta, and work downstream along some 405 miles of the river's run to Suisun Bay.

The work will start with crew members wading in the river with a backpack-mounted camera setup. The volleyball-sized camera head includes 11 high-definition video cameras that will collect a continuous, 360- degree picture of the river.

When the water becomes too deep to wade, the equipment will be transferred to a kayak or canoe, then a motorboat.

Still images for the "riverview" panorama will be edited out and attached to map points later.

Criscuolo said water samples will be taken at regular intervals, perhaps every mile, and analyzed later to provide water-quality data that will be connected with the maps and images. Data from a number of USGS monitors, which have been fixed in the river for years, will also be integrated.

The group plans to survey 27 rivers in a similar manner. The San Joaquin and Colorado will be next.

It opted to start with the Sacramento River because Criscuolo and his partner, Kristian Gustavson, already know it fairly well because they kayaked its full length in 2009. They also recognize its importance as the source of nearly half of all the fresh water in California.

"We found out that a lot of people depend on the Sacramento River," Criscuolo said, noting that this includes himself as a resident of San Diego, which relies partly on drinking water diverted from the river. "It's a critical artery, and there's a lot of pressure on it."

He expects the end product to be useful not only for planning excursions on the river – whether boating, fishing or paddling – but also to policymakers engaged in big decisions. Those are myriad and ongoing, from flood protection to habitat enhancement, to salmon restoration and flow management.

For example, he said, anyone concerned about salmon habitat could click a map point on the river, find out whether water temperatures are suitable for salmon, and use the images to look for signs of erosion or pollution problems.

For those reasons, the Sacramento River Watershed Program is helping Criscuolo connect with local groups that depend on the river and might have an interest in the results. The nonprofit program has been working since 1996 to restore and sustain the river for all its users.

"Pictures tell a thousand words," said Mary Lee Knecht, executive director of the watershed program. "We think the visual aids this project will come up with will help us understand how the river is changing, and how those changes affect the ecosystem as well as the landowners along the river."


Effort to Boost Salmon Numbers Weakens Wild Fish

Study finds 90 percent of salmon in a Northern California river were raised in hatcheries

By John Upton
The Bay Citizen
February 8, 2012

Chinook salmon swimming up the Mokelumne River are lured into a trap, killed and gutted of their eggs and sperm, which are blended in jars. State workers rear the hatchlings that emerge from the eggs, and then truck the young fish to a stretch of the San Joaquin River near the Antioch Bridge, where they are poured into the water.

The efforts have succeeded in replenishing depleted salmon populations, but the hatchery-raised fish may actually be weakening the ranks of wild salmon, according to research published Wednesday. Wild salmon have almost entirely disappeared from the river, replaced by their reared-and-released cousins, the scientists discovered.

The hatchery practice is long-running and widespread — the California Department of Fish and Game operates 21 salmon and trout hatcheries, the first of which opened 102 years ago.

Mokelumne River Hatchery, in the Central Valley town of Clements, last year reared and released steelhead trout and more than 5 million salmon, using funds from the sale of commercial fishing licenses and from the East Bay Municipal Utility District to offset the impacts on the species of a dam that it operates.

Researchers analyzed the ear bones of fish to determine whether they were raised in the wild or in a hatchery.

“The ear bone grows with concentric rings, sort of like a pearl in an oyster,” explained Peter Weber, a geochemist at the Lawrence Livermore National Laboratory and co-author of the study. “Those rings can be used to figure out the chronology of the life of the fish.”
The scientists discovered that just 4 percent of the fall-run salmon swimming through the Mokelumne River watershed in 2004 had been reared in the wild. Within the actual river, not including its tributaries, 10 percent were found to be wild. The rest began their lives in a hatchery. The discovery was scheduled to be reported Wednesday in the online journal PLoS ONE.

“It just goes to show that it’s actually not a sustainable population,” said Rachel Johnson, a fishery biologist affiliated with the Institute of Marine Sciences at UC Santa Cruz and with the U.S. Bureau of Reclamation. “The babies that are born in the rivers aren’t surviving enough to come back and replace their parents.”

Johnson, the principal author of the report, said wild-born salmon enjoy greater success as parents in the wild, either because they are better at breeding or because their young are physically and genetically stronger. A salmon population dominated by hatchery-reared specimens could be weakened, she said.

The scientists made the discovery by taking advantage of slight chemical differences in sulfur contained in food eaten by wild and hatchery-raised fish. Fish born in a river eat freshwater food when they are young, while hatcheries generally use feed that comes from the ocean, Weber said. Those differences show up in the ear bones.

The Bay Area and Central Valley mark the southernmost range for Chinook salmon, which hatch in rivers as far north as Alaska before taking to the Pacific Ocean to feed and grow over several years. Under natural conditions, they use scent to help them navigate back to their natal stream to spawn and die, although research indicates that hatchery-raised salmon struggle to locate the rivers into which their parents swarmed.

The local populations of Chinook salmon were decimated in recent decades, leading to the closure of the state’s salmon seasons in 2008 and 2009. Fish numbers have recovered since that time, although they are still far below their natural levels.

Christina Swanson, director of the Natural Resources Defense Council’s science center in San Francisco, said the main reason that the species struggles to survive is the succession of dams that have been built throughout the state’s rivers to trap drinking water and generate hydroelectricity. The dams prevent salmon from reaching their natural spawning grounds.

“For the most part, the declining stocks are a combination of steadily declining freshwater conditions and of course having been blocked from a lot of their habitat,” Swanson said, adding that poor ocean conditions also take a toll.

“Salmon are one of these wonderful species that are entirely dependent upon multiple ecosystems and habitats in order to complete their life cycle,” Swanson said.
The salmon shortage makes life difficult for fishermen, and it also makes it hard for upstream plants and animals to find food.

“Predators and carrion feeders would eat them. The dead bodies would fertilize the shores of the river and be absorbed by the plants and the forests,” Swanson said.


Celebrated Marin County salmon make their return

Peter Fimrite
San Francisco Chronicle
February 3, 2012

The storied silver salmon of West Marin - long considered a bellwether of salmon health in California - are laying eggs and carrying on in Lagunitas Creek this week almost as if they weren't teetering on the edge of doom.

There are, of course, plenty of obstacles to the species' long-term survival, but last month's long-awaited rain - paltry as it was - prompted the endangered fish to begin their annual rush into the creeks and tributaries of the lush San Geronimo Valley to make babies.
The late blitz of coho brought renewed hope to fisheries experts, watershed managers and the creekside communities where the celebrated fish lay their eggs and then die.
"It shows that these fish can survive for months without spawning, while waiting for the rains to come," said Eric Ettlinger, the aquatic ecologist for the Marin Municipal Water District, which conducts annual fish surveys with help from volunteers and nonprofit groups. "Three years ago people were discussing how coho were about to become extinct in Central California, and it seems like they are beginning to bounce back."

Strong turnout

Biologists have observed 377 coho salmon in the Lagunitas watershed this winter and 103 redds, the word used by brainy types in smocks to refer to the clusters of pink eggs that salmon lay in the gravel.

It is a remarkable showing, Ettlinger said, considering the lack of rain this season. The salmon, he said, have been waiting since November for creek flows to be strong enough for them to swim up to their favored nesting spots. The carnal surge began Jan. 19, when the region was doused by 10 inches of rain.

Coho, also known as silver salmon, are born in cold freshwater rivers and streams where they live for a year before swimming to the ocean. They typically return at age 3 to where they were born to lay eggs and fertilize them.

This year's fish are the children of the 2008-09 generation, which holds the record for the least fertile since the district began the surveys 17 years ago. Only 43 coho and 26 egg nests were seen in the watershed that year.

"The fish that are spawning now are the offspring of those few fish," Ettlinger said. "We are very pleasantly surprised at how many of those offspring have returned."

Last winter, 152 coho and 80 redds were counted in the watershed, which includes Lagunitas and San Geronimo creeks. That was disappointing, Ettlinger said, because the fish were the grandchildren of the coho that spawned in 2004-05, the most potent generation on record. The 1,342 coho seen in the watershed that year made 496 redds.

Fearing for the fish

In fact, the past three years were the least profligate spawning years on record, raising fears among biologists that the species was in the midst of a death spiral.

"Last year marked two generations of steep declines," Ettlinger said. "Those years were all lower than their parent generations were. Now, for the first time in seven years, we are seeing more offspring than the parent's generation."

The Lagunitas coho swim 33 miles through the redwood- and oak-studded valley on the northwest side of Mount Tamalpais. It is the largest wild run of coho salmon along the area that biologists and regulators categorize as the Central Coast and is a model for fisheries restoration in the state.

Marin County has always been a stronghold for coho, which were so numerous that grizzly bears fed on them before Europeans arrived in California. Legend has it that homesteaders speared them from docks over the water. The runs kept up even after 1873, when the first of seven dams were built in the watershed, blocking 50 percent of the historic spawning habitat.

Then, suddenly, the fish stopped showing up. Central California coho were listed as endangered in 2005 under the U.S. Endangered Species Act.

The Lagunitas run is unique not only because all the fish are wild - a large proportion of the coho in other places are raised in hatcheries - but because their primary spawning grounds are in the middle of developed communities. Some 40 percent of the coho in the watershed are hatched in tributaries surrounded by homes, golf courses, roads and horse corrals in the 9-square-mile San Geronimo Valley.

The jacks come home

Ettlinger said there are signs that things are improving. Biologists have spotted a lot of jacks, the small male salmon that return to their natal streams one year earlier than their siblings.

The number of jacks in any given stream is a good indicator of how many fish will return the next year.

"Just last week more than half of the salmon we saw were jacks," he said. "This suggests that there are many, many more of their siblings out in the ocean that will, hopefully, return next year."

Ettlinger said the virility of the salmon this winter despite the difficult circumstances "speaks to the resilience of the species that they can withstand fairly adverse conditions."
He said their survival is also a testament to the dedication of local citizens, schools and community leaders.

"This watershed has a really active volunteer community that does restoration work and creek hikes," he said. "There is a lot of support for the salmon within the watershed."

Coho salmon (Oncorhynchus kisutch)

Range: Coho are found on both sides of the North Pacific Ocean from Hokkaido, Japan, and eastern Russia, around the Bering Sea to mainland Alaska, and south all the way to Monterey Bay.

Description: Adults typically weigh 8 to 12 pounds and are 18 to 30 inches long, though individuals weighing 31 pounds have been caught.

Life cycle: Anadromous, meaning adults re-enter natal freshwater streams to spawn after spending half of their three-year life cycle in the salty Pacific. Adults die within two weeks of spawning. Fry grow to 4 to 5 inches long before heading to the Pacific.

Sources: Marin Municipal Water District, National Marine Fisheries Service, ESRI, GDT and Alaska Department of Fish and Game.

Seeing salmon

The best coho viewing areas in the Lagunitas Creek watershed:
Leo T. Cronin salmon viewing area: Just off Sir Francis Drake Boulevard where the Shafter Bridge goes over Lagunitas Creek near Samuel P. Taylor State Park. Fish can also be seen from the Shafter Bridge at the Inkwells, a series of small waterfalls along San Geronimo Creek.

Roy's Pools: Salmon demonstrate their jumping skills in three pools below the former dam site, on San Geronimo Valley Drive, 5 miles west of Fairfax.

Samuel P. Taylor State Park campground: Coho like to lay their eggs behind the park headquarters building, just off Sir Francis Drake Boulevard.


Supervisors hear salmonid conservation program update

By John Bowman
Siskiyou Daily News
January 19, 2012

Yreka, Calif. —

Richard Harris, Ph.D and Sandra Perez of the Five Counties Salmonid Conservation Program (5C) told the Siskiyou County Board of Supervisors on Tuesday that, since 1998, there have been a lot of improvements in county policy and procedures regarding roads and their impacts on salmon.

The 5C staff was at the meeting to present the results of a reassessment of county policies and procedures throughout the program area.

The 5C program began in 1997 when the five counties of Del Norte, Humboldt, Mendocino, Siskiyou and Trinity agreed to collaborate on a proactive response to the ESA listing of coho salmon as a threatened species.

“The primary 5C goal is to strive to protect the economic and social resources of northwestern California by providing for the conservation and restoration of salmonid populations to healthy and sustainable levels and to base decisions on watershed rather than county boundaries,” the 5C website says.

In 1998 the program completed an initial assessment of policies, procedures and conditions with the potential to impact salmonid populations within the five counties, focusing primarily on road related impacts. According to 5C, that initial assessment has guided the 5C program and its restoration efforts – including fish passage improvement and sediment reduction – ever since.

In 2007 the program began the first phase of a reassessment of policies, procedures and conditions. The goal of the reassessment was to determine if the procedural and policy changes as well as restoration efforts undertaken have resulted in improvements over conditions observed in the initial assessment 10 years earlier.

According to Perez, fish passage and sediment reduction have been the two major focal points of the program since the beginning.

Harris explained that there were two phases to the reassessment.

“The first phase was an evaluation of all the policy changes that had occurred in the five counties since 1997,” Harris said. “That means changes to general plans, general ordinances and state regulations.”

The phase one report was published in 2008. He said there have been a lot of changes at all levels of government since the initial assessment in 1998.

The second phase of the reassessment, Harris said, was an evaluation of practices “on the ground.” He estimated the phase two final report will be published within a month.

Harris listed a variety of improvements observed throughout the five county area. In regards to Siskiyou County, he specifically noted the county’s efforts to create a land development manual and the fish-centric consciousness and care taken by the roads department in their emergency response practices. Harris also added that Siskiyou County is “ahead of the curve” in the area of streambank stabilization.

One of the main findings of the reassessment, Harris said, was the recognition of what he called the “regulatory morass.” He expressed frustration with regulatory agencies’ unwillingness to ease regulatory requirements for in-stream projects intended to improve conditions for salmonids.

“We’re doing beneficial projects and yet the same regulatory process applies as if you were doing a project that’s going to impact fish,” Harris said. “It doesn’t make any sense to me.”
Harris and Perez said the recommendations resulting from the reassessment were not specific to any one county. One of the recommendations that were recurring in several categories was the streamlining of permitting for projects benefitting salmon.

Recommendations also included investigations into the cumulative impacts of unregulated or illegal surface grading, driveway or road cutting and water diversions. In addition, 5C recommends counties continue to refine their Best Management Practices (BMPs) policies and continue to have county staff attend 5C-sponsored trainings.

Harris told the board that in the other counties, illegal earth moving and water diversions from marijuana propagation are a substantial threat to salmonid habitat.

Siskiyou County natural resource policy specialist Ric Costales asked, “At what point are you guys going to say everything that can be done has been done, and essentially the focus is no longer on the county roads department?”

Harris said he doesn’t have a good answer for that question and shares Costales’ frustration. He refered to the state water pollution regulatory process known as the Total Maximum Daily Loads (TMDL) rhetorically asking, “When have you changed from non-attainment to attainment? And who’s going to determine that and on what basis?” He added, “I think the TMDL process is a sorry substitute for good stewardship.”

District 5 Supervisor Marcia Armstrong said, “We’ve been beating our heads against the wall trying to help salmon and we get nothing for it except kicked in the face. It’s not a matter of salmon anymore, it’s a matter of controlling us and pushing us off the land.”

District 3 Supervisor Michael Kobseff said he appreciated the good news that the county is doing a good job in managing its roads and commended the roads department on their efforts. He requested that 5C assist the county in getting that message out to state regulators and legislators.

District 2 Supervisor Ed Valenzuela said he feels that regulatory relief is a high priority.
“We’ve done a lot of projects here and we’ve done a lot to do the right thing,” he said. “I think that’s under-reported, understated and under-appreciated by the environmental side.”


Viewpoints: State has stake in Columbia salmon solution

By Zeke Grader
Special to the Bee
January 17, 2012

The story of Pacific salmon has not recently been a happy one. Population declines in the West Coast's big three rivers – the Sacramento-San Joaquin, Klamath and Columbia-Snake – have meant less fishing, lost jobs, scarce fish and higher prices for consumers. Without major changes to how we manage these waterways, the beating heart of our region's salmon economy may cease.

Fortunately, there are some bright spots on the horizon. On a growing number of rivers, adversaries are opting to collaborate rather than litigate. People are starting to work together to restore rivers, recover salmon and rebuild jobs.

On the San Joaquin River, for example, city leaders, farmers, fishermen and conservationists ended decades of litigation when they sat down together to craft a plan they all could live with. U.S. Sen. Dianne Feinstein then shepherded the plan through Congress. It has restored water – and salmon – to a 60-mile stretch of river, reconnecting it to San Francisco Bay for the first time in 70 years. Twenty exhausting years of conflict are over.

Farther north, farmers, fishermen, Native American tribes and others have made important progress working together to secure a future for farming and fishing based on a plan that will restore the Klamath River by removing four dams.

Finally, as the result of successful collaborations in Washington state, three dam removals commenced this fall on two other salmon rivers. After resolving issues such as energy and water quality, both the Elwha and White Salmon rivers will flow freely for the first time in a century and provide habitat to struggling salmon runs – benefiting our region's ecology and its economy.

Our next big opportunity to restore salmon and jobs rests on the lower Snake River in eastern Washington. The Columbia basin was once the world's most productive salmon watershed. The Columbia River's largest tributary, the Snake, once produced nearly half of this abundance. Today, thousands of miles of pristine habitat remain, much of it in the wilds of central Idaho. Unfortunately, four dams on the lower Snake make passage lethal for migrating salmon. Completed in the 1970s, these dams are the straw that broke the camel's back. After the dams' construction, all Snake River salmon populations plummeted.

The government's Columbia basin restoration efforts to date have failed both fish and fisherman. Last summer, a federal judge rejected the Obama plan – the fourth to be deemed illegal since 1995. Our government has spent $10 billion over two decades on largely ineffective measures. Faced with a court order to produce a new plan within two years, the same agencies responsible for this series of illegal plans are poised to repeat the mistakes of the past.

Following on these other restoration success stories, it's time for President Barack Obama and our elected leaders on the West Coast – including Gov. Jerry Brown and Sens. Barbara Boxer and Feinstein – to support a stakeholder process to address the needs of Columbia basin salmon and the jobs they support.

Success will require fresh ideas. The process must be guided by science and law, and engage the actual stakeholders – including farmers, fishermen, power producers and consumers – whose lives and businesses are affected by salmon restoration efforts.

Support for an approach like this for the Columbia basin is growing. Late last year, for example, more than 50 members of Congress – including 20 from California – sent a letter to the president urging him to convene a regionwide "solutions table" in order to restore salmon and meet community needs.

California will need a seat at this table. Many of our state's salmon fishermen hold licenses in states across the coast, where many Columbia/Snake River fish are harvested. Owning multiple fishing licenses is critical for businesses in an industry known for its ups and downs.

In addition, because salmon from these different rivers mix in the saltwater, fishing regulations have been set up to protect the most vulnerable runs. Therefore, in order to truly restore a vibrant commercial salmon fishing sector on the West Coast, we need to restore healthy, self-sustaining and harvestable populations on all of our "big three" rivers.

Establishing a stakeholder process to resolve the conflicts on the Columbia is the next big thing for salmon fishermen. California needs to be part of this solution. Recent history demonstrates that these processes can work, and, done right, the benefits that accrue help not only fishermen, but farmers, energy producers and local communities, too.


Agencies OK rock barrier for fish

By Alex Breitler
Record Staff Writer
January 13, 2012

Baby steelhead swimming down the San Joaquin River might have a better chance of reaching the ocean this spring, after state and federal agencies agreed to install a rock barrier at the head of Old River, near Lathrop.

Typically, fish heading down the San Joaquin toward Stockton make a left turn into Old River, which draws them into the south Delta and perilously close to enormous pumps that send water to distant reaches of California.

The rock barrier will keep those fish in the San Joaquin, hopefully steering them away from the pumps.

The agreement, announced Thursday, is an admittedly "limited" truce in the ongoing legal conflict over fish protections versus water supply. It will be in effect in April and May only.

"We believe that this method of reaching an agreement will help lay the groundwork for future collaboration," said Jane Lubchenco, administrator of the National Oceanic and Atmospheric Administration, which includes a fisheries agency charged with assisting oceangoing fish such as salmon and steelhead.

The agreement could help "build additional trust," added California Natural Resources Secretary John Laird.

"Rather than individual parties retreating to a courtroom, we can strive for science guiding us outside of the courtroom," he said.

In addition to the barrier, officials will put in place more flexible guidelines about the backward flow of the Old and Middle rivers. Those streams typically flow in reverse toward the pumps, sucking fish toward their demise. Limiting the degree of reverse flow can protect salmon and steelhead, but it can also limit the amount of water available for cities and farms.

With broader parameters, the experiment might actually result in a modest increase in the amount of water available for export, said Mark Cowin, director of the state Department of Water Resources. At least, that is, compared with the amount of water available under a set of fish protection rules that were thrown out in September by a federal judge.

But, Cowin added, "This in no way is the ultimate answer for water supply reliability for California."

One group not consulted in the agreement was the South Delta Water Agency, including farmers in the Old River area. Blocking off the river with a rock barrier can have "serious consequences" for downstream farmers, attorney John Herrick said in an email Thursday.

But the plan does include up to eight culverts in the rock barrier to ensure there is still flow into the south Delta to maintain water quality for farmers, officials said.

Agencies have experimented with another kind of barrier on Old River: a curtain of bubbles that the fish seem to prefer to avoid. The bubble curtain still shows promise, officials said Thursday, and testing continues.



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Watershed Conservancy
P.O. Box 606, Manton, CA 96059


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