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California Salmon Snapshots Blog

  • Lagunitas Creek Spawner Update: A Glass-Half-Full/Glass-Half-Empty Situation

    January 18, 2017

    Marin Municipal Water District by Eric Ettlinger, Aquatic Ecologist

    The current state of affairs in Lagunitas Creek can be described as a glass-half-full/glass-half-empty situation. Or more accurately, a reservoir-full, streambed-empty situation. By the end of December the coho salmon run was on track to be larger than the parent generation of three years ago and continue the generational improvements we’ve seen for each of the last five years. But then came the unrelenting storms of the last two weeks. On the positive side those storms filled MMWD’s reservoirs and produced the high flows that can create and improve salmon habitats in Lagunitas Creek. On the negative side those flows destroyed many coho redds, washed away some of our salmon habitat structures, and severely hampered our survey work. We’ve heard rumors of fresh coho out there (and steelhead should be starting to spawn too), but we haven’t been able to see them ourselves.

    The most recent storm raised Lagunitas Creek flows to 4,300 cubic feet per second, which was the third-highest flow in 35 years. In the coming months we’ll see if this flood had significant impacts on incubating salmon eggs and/or last year’s fry. Previous major floods in 1998 and 2006 resulted in very poor egg survival, and we expect to see relatively few fry again this summer. One-year-old juvenile coho have survived recent large floods successfully, likely by seeking out slow water areas on floodplains. Ironically, it may be moderate storm events that are most deadly, because flows stay confined in the stream channel and slow water habitats may be hard to find. This summer we’ll be enhancing a number of areas on Lagunitas Creek to provide exactly those kinds of slow water habitats. On an optimistic note, the floods this season have risen and receded rapidly, hopefully subjecting coho fry to fast, confined flows only briefly. In late March we’ll start counting the surviving smolts as they migrate to the ocean and, one way or the other, that data will contribute to our understanding of how salmon survive floods and what we can do to help.

    Topics: blog

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  • Rain and salmon have arrived early in the Lagunitas Creek watershed!

    November 21, 2016

    Marin Municipal Water District by Eric Ettlinger, MMWD Aquatic Ecologist blog.

    Rain and salmon have arrived early in the Lagunitas Creek watershed! So far this year we’ve received over ten inches of rain, with the first major storm of the season hitting on October 25.

    The first spawner of the season, a Chinook (a.k.a. “king”) salmon, was seen migrating on October 27. Since then Chinook salmon have been seen throughout Lagunitas Creek and as far upstream as the town of San Geronimo.

    Chinook don’t show up in Lagunitas Creek every year and are more commonly found farther north and in larger rivers. As of November 17, we’ve counted 21 Chinook redds (gravel nests), which is already the most seen in over a decade.

    Some of these fish were likely part of the large smolt emigration in 2015, but we’ve also seen a couple of fish lacking adipose fins – a sign that they started their lives in a hatchery. California Department of Fish and Wildlife staff are currently surveying Lagunitas Creek to find some of these Chinook carcasses and determine their origins.

    In addition to Chinook salmon, a few coho have also been detected, including a couple counted by MMWD’s PIT tag antenna near Point Reyes Station. It’s still early in the season for coho, but the rain forecast for this weekend will hopefully encourage more coho to migrate upstream and spawn.

    Topics: blog

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  • Allocating a Share of San Joaquin River Water to the Environment Shows Promise

    November 14, 2016

    By Jeffrey Mount, Brian Gray, Ellen Hanak, PPIC Water Policy Center, Peter Moyle, UC Davis Center for Watershed Sciences

    In September 2016, the State Water Board released its draft plan for new environmental flow requirements in the San Joaquin River watershed. The board’s proposal contains a novel—and controversial—recommendation. Instead of following the traditional approach of setting minimum flows to meet specific environmental needs at specific times of the year, the board proposes to allocate a block of water each year to improve habitat for fish and wildlife in the lower San Joaquin River and its tributaries—the Stanislaus, Tuolumne, and Merced.

    As we have argued in several recent reports, assigning a block of water to the environment has numerous advantages over the traditional regulatory approach. Done well, it could improve ecosystem performance and the efficiency of environmental water use, while reducing uncertainty for other water users.

    Here we outline the essence of the board’s proposal and describe its strengths and areas for improvement. We conclude with some suggestions for how these ideas could be incorporated fruitfully into settlement negotiations with stakeholders in the watershed.

    The board’s proposal: Allocating a share of water for the environment

    Native fishes in the Lower San Joaquin River and its tributaries—particularly salmon and steelhead—have been declining for decades. The board has authority to address this decline by setting flow requirements to protect beneficial uses of California’s waters. This authority derives from a variety of California laws that are not dependent on either the federal Clean Water Act or the Endangered Species Act.

    For fish, the board traditionally sets minimum flow standards tailored to meet the requirements of specific life stages of each of the protected species (e.g., pulse flows to facilitate migration up and down the river, cold water for eggs and young fish). These flows are made available through a combination of releases from reservoirs and limitations on diversions by other water users.

    The proposed new approach is to allocate a portion of the February-through-June “unimpaired flow” on the Stanislaus, Tuolumne, and Merced tributaries to native fish. Unimpaired flow is the volume of water that would be present in the tributaries without reservoirs or diversions.

    The plan proposes that an average of 40% of this flow—with a range of 30-50%—be assigned to meet environmental objectives. We have no position on the merits of this proposed share, which is likely to be a matter for negotiation on each tributary.

    More important is the flexible way that environmental managers could use this water. Under the proposal, they could shift flows as needed for different hydrologic conditions or locations to meet biological goals for protected species. This could include storing water for pulse flow releases—such as to improve water quality or provide migration cues for fish—and holding water until late summer to bolster cold water releases from reservoirs.

    Why this approach is a good idea

    The board’s proposal to allocate a flexibly managed block of water to the environment is an improvement over the traditional setting of minimum flow standards in three ways:

    ◾Efficiency: The block approach allows for better use of environmental water to benefit fish. Managers can more easily adapt to changing conditions such as droughts and floods, time flow releases for maximum effect, vary the way they apply water from year-to-year, and more nimbly respond to new biological and ecological information. This would increase the efficiency of environmental water use while also improving its effectiveness.
    Predictability: A block of water is simple, transparent, and easier to incorporate into environmental and operations planning. Assigning a specific quantity of water to environmental uses would give more certainty to other water users, because they would know the percentage of unimpaired flow available to them.

    ◾Shared responsibility: Allocating a flexibly managed block of water to environmental uses would ensure that the environment is better integrated into the water rights system. Environmental water managers would have a seat at the table in water management, deciding how best to use their allocation just as other water users do, and the environmental water block would share equally in abundance and shortage along with other beneficial uses.

    What would make this approach even better

    In addition to this novel approach to establishing flow standards, the draft plan encourages stakeholders and interested parties to negotiate settlements that they would submit to the board for approval. Such negotiations are a good way to harness local knowledge, creativity, and cooperation.

    We recommend that negotiators and the board retain the idea of allocating a block of water to the environment and consider several improvements:

    ◾Allow carryover: The draft plan requires that all environmental water be used in the same water year. To enhance efficiency and to hedge against drought, it should be possible to store some environmental water in surface reservoirs or groundwater basins (with rules to avoid impacts to other users). A good example of the benefits of integrating groundwater and surface water storage with environmental flow management comes from the Yuba River watershed in northern California.

    ◾Allow trading: Environmental water efficiency also would be enhanced if the plan explicitly allowed the buying and selling of this water. A good example comes from Australia, where environmental managers regularly lease some of their water to fine-tune flow management in different catchments. Some revenues from leasing are also used to support ecosystem investments.

    ◾Encourage augmentation: The existence of a well-managed environmental water budget would present an opportunity for better employing conserved urban and agricultural water for environmental purposes. Allowing the budget to be easily augmented with water acquired on a permanent, long-term, or temporary basis through voluntary purchases or donations would increase resources for environmental management.

    ◾Assign responsibility: The proposed governance structure for environmental water management is a large, multi-party committee of regulatory and planning agencies, project operators, water users, and other stakeholders (Draft Plan, Appendix K, page 32). This structure is cumbersome and lacks the independence and flexibility needed to administer the block of water in a timely fashion. The revised plan should create an environmental water manager—perhaps similar to the environmental water holder in Victoria, Australia—with authority and staffing to administer the environmental water for defined biological objectives.

    ◾Improve planning: The long-range biological goals and objectives—beyond improving salmonid populations—are not well articulated in the current plan. Management of the Stanislaus, Tuolumne, and Merced tributaries needs an overarching biodiversity plan that takes a broader, ecosystem-based approach and defines how the environmental water allocation would benefit salmonids as well as other riverine, riparian, and wetland species. The plan should achieve multiple environmental benefits from the water, focusing on different priorities in different types of water years. Such a plan could be developed relatively quickly, based on available scientific information and with input from stakeholders. The biodiversity plan should be revised every 7-10 years, based on improvements in scientific understanding of ecosystem performance. Victoria, Australia provides a model for developing pragmatic, ecosystem-based plans to maximize the benefits of environmental water.

    ◾Monitor and Adapt: It is critical that management of the environmental water allocation be supported by a robust, transparent, and science-based monitoring program. This program should report to the environmental water manager, who would use the information to guide annual allocation and use decisions, adaptation and management experimentation, and long-term planning and evaluation. Funding this effort may require pooling of resources among agencies and water users.


    The board’s proposal to use a percentage of unimpaired flow as an environmental standard and budget for the Stanislaus, Tuolumne, and Merced tributaries has generated a great deal of controversy in the water-user community. While this is understandable, we encourage all interested parties to carefully examine the merits of this approach and to consider its compensating advantages. Block allocations of environmental water—flexibly managed and supported by science, sound governance, and planning—can be an effective tool for achieving the twin goals of ecosystem protection and water supply reliability. Negotiating settlements that seek to achieve multiple benefits from blocks of environmental flows is a promising direction for using California’s water more efficiently and effectively.

    Topics: blog

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  • Thinking big, starting small

    July 7, 2016

    Trout Unlimited by Sam Davidson

    In 2006, the Pajaro River on California’s central coast came out of obscurity to make national headlines—for the wrong reason: it was named the most endangered river in America.

    Historically, the Pajaro was one of the most productive steelhead streams in this region. Old-timers in Watsonville and other local communities recall chromers stacked like cordwood in the holding water as they came in after winter storms blew open the sandbars at the river mouths.

    But water diversions, widespread habitat loss and degradation, and drought reduced this river’s once robust run of wild steelhead to a shadow of its former self.

    Local fish advocates, led by the indefatigable Herman Garcia and his group Coastal Habitat Education and Environmental Restoration (CHEER), sprang into action. By 2006, Garcia and CHEER already had been working for a decade to keep the Pajaro’s dwindling steelhead run alive, through fish rescues and work with landowners to restore aquatic and riparian habitat.

    The Pajaro might seem an unlikely place to invest in bringing back the iconic freshwater sport fish of the Pacific Northwest. Much of the river is bordered by fields of row crops. Its last few miles are now characterized by homeless encampments and large levees.

    Only in the uppermost headwaters do you find the kind of habitat that inveterate steelhead anglers might associate with productive steelhead streams: towering redwoods, firs and maples, freestone creeks, and good substrate in the stream channel. But even here, thirsty residential development combined with drought has diminished the summer streamflows young steelhead need to survive.

    A new video from Trout Unlimited shows that, despite the river’s many challenges, the potential for successful habitat restoration in the Pajaro is strong.

    That’s because in 2009 TU, CHEER, and the Center for Ecosystem Management and Retoration (CEMAR) teamed up to "think big and start small” in restoring steelhead habitat in the Pajaro.

    It’s also because the watershed has another critical ingredient for restoration success: landowners willing to work in partnership with
    groups like TU and CHEER to keep more water in-stream during the dry season.

    TU’s new video, Good Neighbors: Sharing water with steelhead on Little Arthur Creek, illustrates the power of these partnerships to make modest changes in water use and storage that have big ecological benefits.

    The Gilroy Dispatch published an excellent article on the Little Arthur Creek partnership.

    This short film tells the story of a landowner—and that of Garcia, who grew up camping, fishing, and hunting on Little Arthur Creek—and how they came together with TU’s California Water Attorney Matt Clifford and our other project partners to start restoring the summer streamflows that will make this key Pajaro River tributary once again a good place for steelhead to spawn and rear.

    The Pajaro River has a long way to go before it is a viable steelhead fishery again. But as this new video highlights, starting small while thinking big can make a real difference for steelhead in California coastal streams—and for the people who live next to them.

    The Little Arthur Creek Residential Storage and Forbearance Project, and this film, were made possible by the following partners:

    •Trout Unlimited - California Water Project
    •The Campbell Foundation
    •The Dean Witter Foundation
    •The California Department of Fish & Wildlife
    •The California Coastal Conservancy
    •The Santa Clara Valley Water District
    •The San Jose Flycasters
    •The Santa Cruz Fly Fishermen


    Topics: blog

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  • All in the Family: Inbreeding at California Steelhead Hatcheries

    May 2, 2016

    Fishbio Fisheries News and Informatio

    Steelhead, the migratory form Oncorhynchus mykiss, once abounded in California's Central Valley. But its populations have crashed from estimates of 1-2 million (McEwan 2001) to a mere 10,000 in the 1990s (NMFS 1996), and this group of steelhead has been listed as "threatened" under the Federal Endangered Species Act (ESA) since 1998. The primary reason for this decline are the dams that have severed access to 80% of the habitat steelhead historically used for spawning and rearing (Lindley et al. 2006). Additionally, hatchery management has been identified as a factor that contributed to the Central Valley steelhead's threatened status (Federal Register 1996, Federal Register 1998). Transferring eggs and fish for breeding among various hatcheries has homogenized the genetics of the steelhead population, and new research also highlights a concerning amount of inbreeding occurring at California steelhead hatcheries. Similar to the challenges posed to Chinook salmon, current hatchery practices threaten the viability steelhead as well.

    One federal and three state-operated hatcheries currently propagate juvenile steelhead to mitigate for the impacts caused by dams. Steelhead from the federally run Coleman National Fish Hatchery and state-run Feather River Hatchery are considered part of the Central Valley Distinct Population Segment, the group of steelhead considered threatened, whereas fish from the state-run Nimbus and Mokelumne River hatcheries are not. However, genetic research by the NOAA Southwest Fisheries Science Center presented at the CalNeva American Fisheries Society meeting in Reno revealed that fish from the Mokelumne River and Feather River fish hatcheries are essentially the same stock, which is a violation of the Endangered Species Act listing. The researchers also found that across all hatcheries, more than half of fish used as broodstock in the Central Valley hatchery programs have at least one full sibling that is also used as broodstock. About a quarter of the mated pairs at Nimbus, Feather, and Mokelumne Hatcheries are first cousins, which results in some amount of inbreeding, and the researchers even discovered that some mated pairs consist of half siblings or full siblings. Such inbreeding could compromise survival or reproductive success of these fish.

    Genetic mixing is observed across O. mykiss populations within the Central Valley complex (Pearse and Garza 2015), and is due to hatchery stocking practices such as transferring eggs and fish between hatcheries for breeding, and releasing hatchery fish off site, or far from the hatchery location (California HSRG 2012). Conservation efforts are wasted when hatchery fish interbreed with wild fish on natural spawning grounds because hatchery genes considered less evolutionary fit than wild genes, and once they are mixed with wild genes, the effects are largely irreversible (Pearse and Garza 2015). Unfortunately, hatchery-origin fish appear to dominate the Central Valley DPS (Lindley et al. 2007): best-available estimates indicate that 60-92% of all Central Valley steelhead smolts outmigrating past Chipps Island in the Sacramento-San Joaquin River Delta are artificially produced (Nobriga and Cadrett 2001, NMFS 2003, U.S. Bureau of Reclamation 2008). and straying hatchery-origin fish represent 63-92% of all (Nobriga and Cadrett 2001).

    The contribution of hatchery salmon can be very high on certain rivers, such as on the American River, where hatchery fish accounted for more than 90% of the O. mykiss at natural spawning grounds from 2002-2010 (California HSRG 2012). These values are much greater than those observed historically; during the 1950s, hatchery fish only comprised about 12% of the total Central Valley steelhead population (Hallock et al. 1961 as cited in Nobriga and Cadrett 2001). Current influxes of these straying hatchery fish can mask the declines happening in natural populations, which begs the question of whether wild O. mykiss populations would be self-sustaining if not for the constant supply of hatchery subsidies.

    Topics: blog

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