Welcome to the California Fisheries Blog

The California Sportfishing Protection Alliance is pleased to host the California Fisheries Blog. The focus will be on pelagic and anadromous fisheries. We will also cover environmental topics related to fisheries such as water supply, water quality, hatcheries, harvest, and habitats. Geographical coverage will be from the ocean to headwaters, including watersheds, streams, rivers, lakes, bays, ocean, and estuaries. Please note that posts on the blog represent the work and opinions of their authors, and do not necessarily reflect CSPA positions or policy.

More on Delta Science

Posted on January 19, 2017 by Tom Cannon

I have written often on Delta science and what has been or could be learned from science to support water management. Yet another biennial Delta science conference, the 9^th, was held this past November. This year’s conference theme was: “Science for Solutions: Linking Data and Decisions.” Another year has passed, and more has been studied and learned. More dots have joined the dozens of previous dots in data charts from annual surveys of Delta organisms and habitat conditions. More dots lament the loss of water and habitat. The huge Delta Science Program has progressed yet another year.

Opening Talk

In Phil Isenberg’s opening talk, “A Guide for the Perplexed”, the former legislator and former chair of the Delta Stewardship Council suggested that scientists learn to smile more. He asked: “Why should science be involved in policy anyway?” He talked about how policy makers view science. (Obviously, many are perplexed.) He forgot that the universe and Mother Nature are vastly mysterious things, which are often more complicated than human understanding, but sensitive to human actions at the same time. Yes, science is perplexing.

Mr. Isenberg talked about “independent science” and “combat science,” as though they were two different things. To borrow a legal term, science is not self-executing. Then he asked: “How do we know when we are using the best-available science”? His answer: “When it is good enough to avoid doing something stupid.” Clearly, we have yet to reach that point. The problem has been in choosing to do the best thing, not that good choices or unknown or not “available.” He then quoted Churchill: “America will always do the right thing after trying everything else first”. At least we have gotten past the point where we thought the world is flat. It is all very perplexing.

Mr. Isenberg concluded by suggesting: “It’s the notion that scientists live looking farther out than the rest of us do with the gift of foresight that if properly utilized, can inform, educate, and ultimately motivate policy makers.” He forgets that ultimately policy makers must trust scientists to get the job done. Example: the Trinity Project and the atomic bomb in the 1940’s. As long as water managers and policy makers lead the science, the Delta’s problems will not be solved.

The Delta Science Program

Clifford Dahm, former lead scientist for the Delta Stewardship Council, spoke on his Delta Science Program, which was forced upon us in the 2009 Delta Reform Act to ensure water and environmental policy are guided by the “highest caliber” science. He spoke on the program’s Independent Science Board, outsiders who meet once a year to review “our science”. He spoke on their Adaptive Management Program, which ensures that we evaluate everything and learn nothing. He spoke on the program’s efforts to coordinate science and inform decision makers, and to develop and implement the Delta Science Plan and promote the Science Action Agenda. He talked about their modeling efforts: “There’s just a lot of ways that modeling could be moved forward, and I hope that in the next two years, we can actually come back to you and say that some of our modeling efforts have shown greater fruition as time goes on. We were talking about the idea of potentially a modeling center or a co-laboratory to get modelers together.” Those would be the two years after which we will have new water quality standards, new biological opinions, and new tunnel-boring machines in the Delta, as well as several newly extinct native fish species. They would also be the two years after 20 years of effort starting with the CalFed Bay-Delta Program.

A Great Question

U.C. Davis fisheries biologist Peter Moyle then addressed the question: “How has your research program and the data it has produced over the last 35 years been used to develop solutions for conserving aquatic resources in Delta?” He quoted the 1998 Strategic Plan:

This strategic plan, if followed, should lead to an orderly and successful program of adaptive ecosystem restoration…. The Strategic Plan Core Team has high expectations for the Ecosystem Restoration Program. There is no turning back and the team anticipates that in 20-30 years many habitats will be restored, endangered species will become abundant enough to be delisted, and conflicts will be lessened , even in the face of population growth and increasing demands on resources.

In addressing the posed question, he then remarked:

In retrospect, now that almost 20 years has past since that was written, the statement almost seems tongue in cheek because clearly that has not happened. I continue to help write reports that recommend how to improve the Delta ecosystem and frankly I don’t see much progress being made, as the delta smelt trends so eloquently attests… the reality is that the Delta has continued to deteriorate as a habitat for native fishes, despite my research and despite many proposals for solutions.

His experience, like that of so many other long-time Delta scientists, is that few if any of the specific recommendations in the Strategic Plan have been implemented or completed. Science has done its job, and scientists have long awaited action. Policy makers and managers have failed us, not the science.

The use of science in complex public policy decision making

Chair of the State Water Board Felicia Marcus spoke on the use of science in decision making. She suggested to scientists: “Dare to recommend, but don’t decree … Retain your scientific integrity but dare to make recommendations. At the same time, own your power and be responsible with it and have empathy for the decision makers who have to balance, even as you would have them respect you.” This is a very tough sell for scientists who have not been listened to for decades. What will she and her Board do with two more rounds of recommendations on the Delta tunnels and the Bay-Delta Plan? Will her Board be as transparent and methodical in their balancing as the scientists are in making their recommendations?

Chair Marcus further stated:

We’re entering the era of adaptive management that requires all of the above as well as integrating social sciences into our work … To make adaptive management work, we all have to learn how to be better ‘egosystem’ managers in order to be better ecosystem managers in the real world over time, versus lurching from sound bite to sound bite or wringing our hands that other players just don’t get it.

Sorry, but that’s not the problem. It gives the policy makers and the managers too much credit and scientists too little. Very few scientists think that managerial ignorance or lack of cognition is the biggest problem. Rather, it’s that scientists have endured decades of adaptive management in which their lessons and caveats have on the whole been subsumed to the social sciences of politics and economics. There are plenty of scientists throughout the resource agencies and non-profit groups who are extremely articulate and who have great senses of humor and social skills. That hasn’t changed the outcomes: fish and other parts of the Bay-Delta aquatic ecosystem are in crisis, and the agricultural economy and other values against which the ecosystem is “balanced” are thriving.. And that balance sheet is really nothing to smile about.

Fundamental Needs of Central Valley Fishes – Part 1c: Spring River Flows

Posted on January 17, 2017 by Tom Cannon

In the coming months and years, regulatory processes involving water rights, water quality, and endangered species will determine the future of Central Valley fishes.

To protect and enhance these fish populations, these processes will need to address four fundamental needs:

River Flows
River Water Temperatures
Delta Outflow, Salinity, and Water Temperature
Valley Flood Bypasses

In this post, I summarize a portion of the issues relating to River Flows: spring flows. Previous posts covered fall and winter flows.

River Flows – Spring

River flows in spring drive many natural ecological processes in the Central Valley related to Sierra snowmelt. Winter-run and spring-run salmon, steelhead, Pacific lamprey, and white and green sturgeon ascend the rivers from the ocean during the spring snowmelt season. Spring-run salmon arre able to migrate upstream in the high water to hold until late summer spawning. Winter-run salmon and sturgeon spawn in the Sacramento River below Shasta that same spring. Pacific lamprey spawn in streams throughout the Valley in spring. Juveniles, and remnant yearlings of all these species spawned in the previous year, head to the ocean in the high flows. In the Valley, the spring snowmelt and rains swell the rivers for the annual runs of Delta smelt, splittail, American shad, Sacramento suckers, and striped bass. In the Bay-Delta, spring flows spur annual productivity that sustains juvenile longfin smelt, Delta smelt, fall-run salmon, green and white sturgeon, striped bass, American shad, and splittail, as well as many resident and estuarine fishes and their food supply.

Much of the Valley’s snowmelt is captured in mountain and Valley rim reservoirs, breaking the link between the ocean and mountains. In the lower Sacramento River below Shasta Reservoir, spring snowmelt flows are markedly reduced by retention of snowmelt in the reservoir (Figure 1). The Feather River, the main Sacramento River tributary, are similarly affected (Figure 2). In the San Joaquin River watershed, absence of flows sourced in spring snowmelt is also severe (Figure 3). The capture of snowmelt not only reduces flow in Valley rivers and the Bay-Delta, but also reduces sediment load, river scour, water depths and velocities. It raises water temperatures and limits the extent of natural floodplain inundation. All of these are important ecological processes on which native fishes depend.

Figure 1. Pre-and post-Shasta flows in the lower Sacramento River near Red Bluff (Bend Bridge gage). Note that nearly all the peak spring snowmelt flows have been removed below Shasta in all year types. (USGS gage data)

Figure 2. Pre- and post-Oroville Reservoir flows in the lower Feather River. (CDWR data)

Figure 3. Spring snowmelt (natural flow – blue line) is retained in New Melones Reservoir except for prescribed irrigation releases and salmon migration flows (orange line – reservoir releases to lower Stanislaus River). (CDEC data)

Under current operations, spring snowmelt into the Valley reservoirs is generally held in storage except for minimum downstream flow requirements, agricultural demands, Delta inflow and outflow to meet water quality standards, and minimum flow specifications for endangered fish in biological opinions. Flow releases for agriculture and fish are generally re-diverted soon after release, thus resulting in further reduction of downstream flows (this is the case for the lower Sacramento River in Figure 1, the lower Feather River in Figure 2, and lower Stanislaus River in Figure 3). Critical conditions often appear below these diversions in the lower Sacramento River (Figure 4), in the lower San Joaquin River, and in outflow from the Delta to the Bay.

What is needed are spring releases (spills) from the major Valley reservoirs to the major rivers below dams that carry at least in part to the Bay, to stimulate and sustain migrations of the adult and juvenile anadromous fish throughout the Valley. Water releases timed to the natural flow pulses would stimulate migration, providing even more flow and stimulus for young anadromous fish from all the Valley rivers to pass successfully through the Delta and Bay to the ocean.

Figure 4. River flow (cfs) in lower Sacramento River below major irrigation diversions in four recent years representing four water-year types. Green line represents minimum flow needed to maintain a semblance of essential ecological processes in the lower river. Red line represents preferred minimum level protecting ecological processes. May-June flow is generally depressed except in wet years.

Winter-Run Chinook Salmon Status – End of 2016

Posted on January 15, 2017 by Tom Cannon

The prognosis for winter-run Chinook salmon is not good following very poor survival of the 2014 and 2015 spawns in the Sacramento River below Shasta Dam. The run had been recovering after the 2007-2009 drought (Figure 1). However, year class production suffered in the 2012-2015 drought, culminating with the year class (spawn) failures in 2014 and 2015 (Figure 2) caused by egg stranding and high water temperatures. Run size and juvenile production/survival estimates for 2016 are as yet incomplete, but production of juveniles as estimated from Red Bluff rotary screw trap data indicates some improvement over 2014-2015.¹ The somewhat higher number of recruits produced in 2013 likely boosted the spawning run in 2016.

With water year 2017 starting out as a wet year with considerable flooding, conditions for the emigration of the 2016 year class should be optimal. If wet conditions persist, spawning and rearing this spring and summer for the 2017 year class should also be optimal. Planned release of 600,000 winter-run hatchery smolts in the coming weeks coincident to high Sacramento River flows also bodes well for the 2016 spawn and the future 2019 run. However, the prognosis for the 2017 and 2018 runs remains in doubt because of the above-mentioned 2014 and 2015 year class failures.

Additional insight into the future is possible by taking a closer look at the population’s spawner-recruit relationship that I prepared for the past four decades (Figure 3). Recruitment appears to be a function of both the number of spawners three years prior to any given year and environmental conditions between spawning and emigration in a given year. (Other factors such as ocean conditions may also add to variability in the data.) The recruits-per-spawner ratio is higher three years after wet years than three years after dry years. The runs in 2017 and 2018 are likely to be severely depressed because of extremely poor 2014 and 2015 recruitment, and may possibly be as low as those produced after the 1987-91 drought (only 100-200 wild spawners).

For further reading on winter-run status see:

Figure 1. Winter-run Chinook salmon escapement (run size) into upper Sacramento River near Redding, CA from 1974-2015. (Data Source: http://www.dfg.ca.gov/fish/Resources/Chinook/CValleyAssessment.asp)

Figure 2. Survival of winter-run year classes below Shasta Dam from 1996-2015. The water temperature standard for the Sacramento River near Red Bluff was weakened during 2012-2015 drought. The severely weakened water quality standard in 2014 and 2015 led to poor survival and virtual loss of two year classes. (Source: http://www.waterboards.ca.gov/waterrights/water_issues/programs/drought/sacramento_river/docs/nmfs_yip_03182016_ppt.pdf)

Figure 3. Winter-run Chinook spawners versus number of spawners three years later (recruits) for years 1974 through 2012. Selected wet year spawn dates shown in blue. Selected dry year spawn dates shown in red.
(Data source: http://www.dfg.ca.gov/fish/Resources/Chinook/CValleyAssessment.asp)

https://www.fws.gov/REDBLUFF/RBDD%20JSM%20Biweekly/2016/Biweekly20161202-20161216.pdf ↩

Splittail Status – End of 2016

Posted on January 13, 2017 by Tom Cannon

The prognosis for splittail was not good in 2015¹ after four years of drought and little recruitment since 2011. The below-normal water year in 2016, with its limited winter flooding, brought no apparent recovery in the Fall Midwater Trawl Index (Figure 1). Summer salvage (Figure 2) indicated that there was some production in 2016, although salvage was two orders of magnitude lower than the previous normal water year 2010 (Figure 3) and three orders of magnitude less than the previous wet water year 2011 (Figure 4).

If water year 2017 were to continue on its current trajectory and become a wet year with widespread flooding, conditions for splittail spawning and rearing this winter and spring would be optimal. A positive response in salvage, Fall Midwater Trawl Survey, and FWS Seine Survey would indicate some form of recovery in the population. However, a lack of response on the order of that which occurred in 2011 would be a signal that the population is in dire straits and at risk of recruitment failure and eventual extinction. In the absence of a 2011-magnitude response in the next wet year, the fisheries agencies should conduct a comprehensive review to evaluate whether to re-list² splittail under the federal and state endangered species acts.

Figure 1. Splittail Fall Midwater Trawl Survey Index 1967-2016. (Data Source³)

Figure 2. Splittail salvage in 2016. Export rate for federal and state pumping plants. (Source⁴)

Figure 3. Splittail salvage in 2010. Export rate for federal and state pumping plants. (Source⁵)

Figure 4. Splittail salvage in 2011. Export rate for federal and state pumping plants. (Source⁶)

http://calsport.org/fisheriesblog/?p=1126 ↩
Splittail were de-listed in 2003. On October 7, 2010, the USFWS found that re-listing of splittail was not warranted (75 FR 62070). The splittail is designated as a species of special concern by the California Department of Fish and Wildlife. ↩
https://www.wildlife.ca.gov/Conservation/Delta/Fall-Midwater-Trawl ↩
https://www.wildlife.ca.gov/Conservation/Delta/Salvage-Monitoring ↩
https://www.wildlife.ca.gov/Conservation/Delta/Salvage-Monitoring ↩
https://www.wildlife.ca.gov/Conservation/Delta/Salvage-Monitoring ↩

Striped Bass Status – End of 2016

Posted on January 11, 2017 by Tom Cannon

The prognosis for stripers was not good in 2015¹ after four years of drought. The normal water year in 2016 brought only minor improvement in recruitment of juveniles into the population, but recruitment remains near record lows (Figures 1-3). The wetter 2016 started with higher juvenile production, but that stalled by late spring. Striped bass salvage at south Delta export facilities showed typical patterns, with about 10% of the numbers salvaged in year 2000 and two primary peaks in salvage – late spring/early summer and late fall (Figure 4).

The Fall Recruitment Index of juveniles into the population as derived from the Fall Midwater Trawl Survey (Figure 2) compared with the prior Summer Townet Survey (Figure 1) indicates a strong positive relationship (Figure 5). The year class strength is very much dependent on the number of young starting the summer, which in turn is likely related to the number of eggs laid in spring and subsequent survival of larvae hatched to the early summer juvenile stage as measured in the Summer Townet Survey. Subsequent survival to the fall appears related to summer habitat conditions, for which a good indicator is Delta outflow. High relative survival to fall in 1998 and 2006 (labeled blue in Figure 5) is likely due to these summers’ higher Delta outflow (Figure 6) and related Delta conditions including export levels (Figure 4). The 2010 and 2016 fall indices were likely suppressed by low outflow, high exports, and resulting poor in-Delta survival, indicated by high salvage numbers. Likewise summer and fall indices in drought years 2007, 2014, and 2015 were likely depressed (Figure 5) by these same factors.

The above patterns and observations are very important because the striped bass remain an important indicator of Bay-Delta Estuary ecological health.

Figure 1. Striped bass Summer Townet Survey Index 1959-2016. (Data Source²)

Figure 2. Striped bass Fall Midwater Trawl Survey Index 1967-2016. (Data Source³)

Figure 3. Striped bass Fall Midwater Trawl Survey Index 2000-2016. (Same source as Figure 2)

Figure 4. Striped bass salvage at south Delta fish facilities in 2016. Export rate is shown as acre-feet (~2 times rate in cfs). (Data Source⁴)

Figure 5. Striped bass Fall Midwater Trawl Survey Index (log10[index+1]) versus prior Summer Townet Index (log10). Select years labeled, with color of number showing year type: blue=wet, green=normal, and red=critically dry.

Figure 6. June through August Delta outflow in 1998, 2006, and 2010.