Category Archives: Bay-Delta

Predator Fish Control Again Rears Its Ugly Head

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The predator-control movement in the Delta got started around the turn of this century when efforts were initiated to reduce the Central Valley Striped Bass population by removing them from Clifton Court Forebay in the South Delta and by stopping the hatchery and pen rearing supplementation programs. Efforts under the Central Valley Project Improvement Act of 1992 (CVPIA), specifically the Anadromous Fish Restoration Program (AFRP), were beginning to make progress at restoring Central Valley fish populations including winter, spring, fall, and late-fall run Chinook, Steelhead, sturgeon, and Striped Bass. Of course, these efforts had been enormously aided by Mother Nature in the form of a series of wet years following the disastrous 1987-1992 drought that precipitated the CVPIA (and many of the endangered species listings).

Striped Bass supplementation had reached its apex. Hatchery raised yearlings were stocked by the millions. Millions of wild young stripers salvaged at South Delta federal and state pumps were placed in pens in the Bay and fed for one to two years and then released.

The end of the wet years and the beginning of the Pelagic Organism Decline in the early 2000s brought out “predator control” for the Central Valley. Federal and state water contractors planted the seed as their Delta diversions reached record levels of 6 million acre-ft. The first effort was to develop a predator removal program at the State Water Project’s Clifton Court Forebay in the south Delta. A further effort forced California Department of Fish and Wildlife (CDFW) to prepare a Habitat Conservation Plan (HCP) for its Striped Bass Supplementation Program (which was approved and the program continued for several years). CDFW did not undertake predator removal in the Forebay.

The 2007-2009 drought brought a water contractor sponsored lawsuit against CDFW, and when that failed, an approach to the California Fish and Game Commission to eliminate sportfishing regulation restrictions on Striped Bass. Relying on sound science, the Commission unanimously rejected their efforts.

The recent Bay Delta Conservation Plan (BDCP) included predator control at “hotspots” in the Delta. But BDCP has been cast aside in favor of Governor Brown’s “water fix.”

This past week FISHBIO Inc., a major contractor for the water districts in the Central Valley, posted “Can Predator Control Help California’s Native Fishes?”1 The post relates the passage of a bill in the House specifically regarding predator control to protect endangered species. While most (hopefully the Senate) will see the bill as part of the water contractors’ “smoke screen”, the bill exemplifies continued efforts on the part of water contractors in the Central Valley to place the blame and solution elsewhere. The post relates about a recent San Joaquin restoration program meeting where information on predators was presented. No mention was made of the recent record low flows in the San Joaquin or the fact that salmon numbers are directly related to flows, or that salmon cannot survive their migrations in the warm polluted waters of the San Joaquin in drier years.

The post mentions a modeling study that shows Striped Bass could eat all the San Joaquin salmon. However, it fails to mention the abundance of young hatchery salmon prey dumped into streams at the same time that Striped Bass and other predators are attracted into the cooler tributaries by the same warm polluted waters of the San Joaquin that block young salmon from moving to the ocean. It fails to acknowledge that upstream dams intercept the early natural pulse flows of cold water that would enable wild salmon fry to move out of the tributaries before waters warm sufficiently for predators to become active. It fails to mention that Striped Bass are also at record low levels. It fails to mention that hundreds of thousands of recovery program hatchery smolts have been dumped into the San Joaquin that serve to encourage predators to switch to salmon (these hatchery fish should be barged to and through the Delta to the Bay – an action that should be funded by the water contractors). And, for the record, it ignores the fact that aquatic life is a mutual eating society and hatchery salmon and steelhead smolts prey on wild salmon fry.

The post concludes with “This month’s actions to amend the Commerce, Justice and Science Appropriation Act may finally open the door to predator control programs in California – a hopeful step towards remedying a long-term problem that continues to spin out of control.” FISHBIO had better prepare for interviews on FOXNEWS.

(AUTHOR’S NOTE: predators including native fishes, birds, and marine mammals, as well as non-native fish like the Striped Bass and other state protected gamefish, take a huge toll on our native endangered salmon, steelhead, trout, smelt, and sturgeon. Predation is probably a primary causal factor as an indirect effect of water diversions on native fish. What is needed is a comprehensive recovery program like that on the Columbia River2. That program addresses the full spectrum predators like pikeminnow, terns, cormorants, marine mammals, and even non-native shad, stripers, smallmouth, walleye, and northern pike. However, unlike California erratic efforts to manage fisheries, the Columbia success-story, at least to date, can be attributed to progressive water management and hatchery-wild fish, science-based, recovery programs.)

Summer 2015 Temporary Urgency Change Petition: Deadly for Delta Smelt

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What does the May 21 TUCP mean for the Delta if the State Board adopts it for the summer? What would be the consequences of weakening the outdated standards for outflow and salinity do to the Bay-Delta ecosystem?

letter

Location of X2 and Delta Outflow

The location of X2, the critical location of the Low Salinity Zone center where salinity is 2 parts per thousand (ppt), is shown below for various Net Delta Outflow Indices (NDOI). The existing standards and proposed changes are as follows:

  • 4000 cfs NDOI in July – 3000 cfs proposed
  • 3000 cfs NDOI August – 2500 cfs proposed for September
  • X2 (2.78 mmhoes EC) required at Emmaton (EMM) moved upstream to Threemile Slough (TMS) through August 15 (no limit thereafter)
Location of X2 in Bay-Delta at various Delta outflows (NDOI cfs).

Location of X2 in Bay-Delta at various Delta outflows (NDOI cfs).

Effect on Water Temperature

In June weakened standards from a previous TUCP were 4000 cfs NDOI, with X2 allowed at TMS. Water temperature at X2 location by mid-June reached 70-73°F, levels considered sublethal but stressful on Delta Smelt.

stressful on Delta Smelt. Early June 2015 water temperatures in X2 region.

Early June 2015 water temperatures in X2 region.

On June 12, 2015, X2 reached Rio Vista Bridge (for first time this year) on high tide after midnight at 72°F (NDOI was 5200 cfs). Afternoon water temperatures at bridge at low tide had been >74°F. When EC was 2000 at TMS, the water temperature was 72°F. On this date in 2012, the X2 location was downstream of EMM, with an NDOI of 7100 cfs and a water temperature of 69°F. On this date in 2013, X2 was downstream of EMM, with an NDOI of 7500 cfs and a water temperature of 68°F. On this date in 2014, X2 was upstream of EMM, with an NDOI of 3150 cfs and a water temperature of 72°F. The pattern is consistent with the hypothesis that the further X2 is east, the warmer the water temperature will be. The pattern also indicates that the normal standard of 7100 cfs keeps water temperatures at X2 below 70°F, at least in late spring.

My prediction for water temperature for July through September in the X2 region is shown below. This conservative prediction is based on June 2015 and June-September 2014 data.

Predicted summer water temperatures in X2 region of the Delta under proposed weakened standards.

Predicted summer water temperatures in X2 region of the Delta under proposed weakened standards.

Consequences to Smelt and Salmon

Delta Smelt, already on the brink of extinction, will be further stressed by near lethal water temperatures in the X2 region. We can assume that only a small number of smelt remain in the X2 zone going into summer 2015, as compared to 2012 (see following charts). Any remaining smelt in the X2 zone must be protected at least at the normal standards as in 2012. Any weakening of the critical year standards will jeopardize the existence of the species.

No Delta Smelt were collected from the X2 zone in late May 2015. Only 5 were collected at the northern Deep Water Ship C

No Delta Smelt were collected from the X2 zone in late May 2015. Only 5 were collected at the northern Deep Water Ship Channel station.”

In contrast to 2015, the distribution of Delta Smelt in late spring 2012 shows higher numbers collected in the X2 zone below Emmaton under NDOIs of 8000-10,000 cfs. Water temperatures at that time in the X2 zone were <70°F.


In contrast to 2015, the distribution of Delta Smelt in late spring 2012 shows higher numbers collected in the X2 zone below Emmaton under NDOIs of 8000-10,000 cfs. Water temperatures at that time in the X2 zone were <70°F.

Fall Run Chinook Salmon enter the Bay-Delta on their spawning migrations from the ocean in August-September. Expected near -lethal water temperature (>77°F) will delay and stress these fish. Expected water temperatures greater than 70°F will stop migrations and degrade subsequent adult salmon pre-spawn survival and egg viability. The proposed 2500 cfs outflow standard for September will result in water temperatures of 73-75°F in the X2 zone near Rio Vista in mid-September. In contrast, in mid -September 2012, outflow was 7100 cfs and water temperatures at Rio Vista and the X2 zone near Emmaton were <70°F.

Delta science – so much talk!

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As we enter the second year of Temporary Urgency Changes for Delta operations, the State Water Board is leaving Delta fish with no protection from our waste and the summer heat while allowing the storage and diversion of millions of acre-feet of water for cities and farms. Little or no water left the Delta for the Bay this spring, and even less will leave this summer. The Smelt Working Group charged with protecting two species of endangered smelt is about to take its summer hiatus as South Delta water temperature hits 25°C. The State Board has recently been forced to reduce Shasta Reservoir agricultural releases for fear of running out of cool water for winter run salmon again this summer.

The State Board’s “drought relief” orders keep little water reaching the Bay and allow salt water to encroach into the Delta. The False River Barrier has been installed to keep salt out of south Delta water diversions at the expense of north Delta habitat. Interior, USFWS, NMFS, EPA, and CDFW, our resource protection agencies, have “concurred” with the Temporary Urgent Change Petitions from Reclamation and CDWR, and the State Water Board has complied. 1

Meanwhile, the remnants of the Delta Smelt population have become isolated in the Sacramento Deep Water Ship Channel. Reclamation scientists assure us that the smelt will be fine and will descend into the cooler water at the bottom of the channel. The lack of smelt in their traditional designated critical habitat of Suisun Bay and the western Delta low-salinity-zone is apparently not a concern.

In the midst of all this “devastation”, the Delta Science Program held a Delta Challenges Workshop this past March.

“On March 16, 2015 the Delta Stewardship Council’s Delta Science Program hosted a workshop to summarize the risks and challenges facing the Bay-Delta system. These challenges include a multitude of stressors that threaten our ability to achieve the Delta Plan’s coequal goals. Numerous reviews, reports and articles describe the stressors and risks facing the contemporary Delta, but this information is spread across diverse publications, journal articles, and lengthy technical reports. The information has not yet been presented in a highly concise, readable way by an independent set of distinguished science experts.” 2

 

The Workshop

Dr. Moyle suggested that we prepare for the worst: “We have to prepare for the extinction of Delta smelt: “It seems very likely to happen in the next year or two,” Dr. Moyle said. “The Fall Midwater Trawl index has never been lower, we’re basically not getting any in any of our samples, and then most recently, the Kodiak Trawl sampling has found very few, even in places they normally aggregate.” He noted that the results of the most recent Kodiak Trawl, a survey aimed at catching smelt in the places where they’re supposed to be, and where they have been in the past, were pretty dismal. “They got 6 smelt, 4 females and 2 males. So the smelt are pretty much gone from this system. We don’t know yet but they could easily have reached a threshold that they can’t get back over, that they can’t survive. We need to be thinking now of answers to questions like: how will we know when the smelt is extinct in the wild? Who declares that? How can the captive populations present in Byron, how can these captive populations be used for re-introduction when better conditions return, at least temporarily, or even should they? And how does management of the Delta change if the Delta smelt are gone? What do we do, essentially, in the absence of Delta smelt?”

Others spoke on adaptive management: “Dr. Goodwin asked Maria Rea about doing large landscape-scale experiments. “To really do an experiment on the scale that needs to be done, and it’s an experiment so you don’t necessarily know what the outcome is, that puts people making decisions in a very difficult position, and I just wonder, how, as a science/policy/management community, what needs to be done to allow these landscape-scale experiments to go on?”

“We do need to get better at experimentation,” Maria Rea answered, noting that with salmon, they’ve done a bunch of tagged fish studies, some with active adaptive management. “The Vernalis Adaptive Management Program had an active component to it, but the number of fish tagged was insufficient to allow any real conclusions to be drawn from that, and so I think we’ve got quite a bit of work to do to. If we’re going to do a large-scale experiment and actually manipulate the system, then let’s make sure we’re growing enough fish and getting enough tags to put in the system that will actually be able to deduce something from the data that we get.”

The need for more money for more science came up: Dr. Luoma noted that since between 1997 and 2010, there was a large injection of science into the system, tens of millions of dollars. “That was a sign of what we need to keep things moving rapidly,” he said. “That money has dried up … If we’re going to really continue on this journey of trying to make progress, it’s obvious we need a big injection of science somewhere managed by the science program. We need an injection of science that allows us all to work together. That’s desperately needed now or else we’re just going to start flailing.”

“We need to explore performance measures, of having something that we can track that helps the policy makers understand the question, what has to happen next. “I think it was Bill Dennison who ran that workshop several years ago, showed us what you can do with a really organized system of performance measures that gets the public involved, gets the policy makers involved. We can do that, we just haven’t done it. I think this is something we really have to focus on doing right.”

Of course, there is always the concept that the Delta continues to evolve and remains hard to understand: Dr. Mike Healey began by noting that one of Jim Cloern’s comments especially resonated with him. “His comment that the Delta is a continually evolving system and we’re never going to be able to fully pin it down. Several people have been talking about wicked problems. Wicked problems have a formal definition in planning and management, and one of the characteristics of wicked problems is that they can’t be solved, they can only be managed. I think that’s probably what we’re looking at is coming up with a system of management that will be hopefully be relatively effective, rather than imagining that we can clearly define this problem and ultimately provide a solution.”

Then there is always the “reality check” and a “happy place somewhere down the road”:
“Once you’ve answered that question, you need to then concern yourself with what’s actually feasible but most of us want something that we’re really not going to be able to get, so we’re going to need to be able to make a reality check and decide what among the things we’d like to have we can actually accomplish, and then the final question is, how do we get to where we want to go from where we are now? And I think we still have a lot of work to do on those latter three questions,” he said. “We’re not anywhere near coming up with the final management plan for this problem as yet, I don’t think,” he said. “But I hope that whatever we can come up with can make some kind of a contribution to making progress, down the road towards that happy place.”

A potential for “boldness” from “outsiders” who can provide a “fresh look” at the problems:
“I really think there is an opportunity here for some boldness, and I hope that we as a foursome will be a bit bold,” he said. “I really do hope that we basically embrace ideas that we can agree upon and present them to you as things that would be the next steps moving forward, or at least our ideas of what that might be, because we need to move beyond just simply continuing to monitor this system. We really need to begin to actually implement some projects, some experiments, and really move that next step down the road to actually beginning to deal with some of the changes that are being imposed on the system and seeing if we can come up with a better and more beneficial ending with some of our attempts. I know it’s fraught with lots of difficulty, and we’re going to make lost of mistakes, but I think we need to be bold and move forward. And hopefully we can give you some ideas on how we think that might be best done.”

And finally, “something learned”, “fun”, and a “ridiculous challenge”:
After public comment, Letty Belin with the Department of the Interior then gave some final thoughts. “I think it’s been an extraordinary day,” she said. “I bet you there’s not a single person in this room that hasn’t learned something significant. I’m still amazed that we got this incredibly talented and experienced panel to accept what I acknowledge is a ridiculous charge. If I had this assignment, I would first turn it back to the teacher and say this is impossible, you cannot summarize this stuff in 15 to 20 pages, and then I’d ask what size can the font be, can it be like .333 but anyway I know it’s particularly fun to hear your reactions and use words like fun.

“I can’t tell you how important I think this effort is,” she continued. “I think it’s going to be incredibly helpful, because policy making in such a complex scientific environment, we need guideposts and people, you all who have both the scientific expertise and the wisdom gained through that, we really are fortunate to be able to get your expertise, so thank you so much.”

Not a word on the drought or changes to Delta water quality standards, or the effects of having no freshwater flow into the Bay.

  1. At a State Board drought workshop earlier this year, the Board chairperson asked the NMFS representative what “concurrence” meant. The NMFS rep responded by stating he had looked up the definition in a dictionary, but they really did not understand its meaning in this case. ↩
  2. http://mavensnotebook.com/2015/04/24/delta-challenges-workshop-part-4-fish-birds-and-habitat/ ↩

Hatchery Reform – Part 2

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Previously… Part 1: Central Valley Salmon and Steelhead Hatchery Program Reform

Environmental Factors Affecting Smoltification and Early Marine Survival of Anadromous Salmonids. 1980. GARY A. WEDEMEYER, RICHARD L. SAUNDERS, and W. CRAIG CLARKE1.

“There is reason to suspect that in many cases apparently healthy hatchery fish, though large and silvery, are not actually functional smolts and their limited contribution to the fishery, even when stocked into the same rivers from which their parents were taken, results from their being unprepared to go to sea. This failure to produce good quality smolts probably arises from an incomplete understanding of exactly what constitutes a smolt, as well as from a lack of understanding of the environmental influences that affect the parr-smolt transformation and which may lead, as a long term consequence, to reduced ocean survival.”

This paper is over thirty years old (1980), yet it still rings true. It is most certainly a complicated subject that is an on-going concern in hatchery science and management. There remains room for improvement if funding is available for hatchery program upgrades.

“In the absence of complicating factors such as altered river and estuarine ecology, smolt releases should be timed to coincide as nearly as possible with the historical seaward migration of naturally produced fish in the recipient stream, if genetic strains are similar. At headwater production sites, much earlier release may be called for… The desired result is that hatchery reared smolts which are genetically similar to wild smolts enter the sea at or near the same time.”

It has been apparent for many decades that Central Valley Fall Run and Spring Run Chinook have a classic “ocean-type” life-history pattern, wherein young spawned in the fall head to the ocean early in their first year rather than as yearlings. Even within the ocean-type, Central Valley Fall Run have two types: one has fry rearing in the estuary (Bay-Delta) and the other in rivers. Of these two types, Valley hatcheries have chosen to manage for the latter. Hatcheries pump out smolts by the millions in April and May, on top of a smaller number of “wild” river-smolts. I believe the “river-smolt” type has been the minority contributor at least since all the dams were built. There simply is not enough river habitat, and what there is has been severely degraded by dams, water management, and physical habitat damage (e.g., levees and land use). The majority contributor is the Bay-Delta or “estuary-smolt” type. Fry that move to the estuary in December-January grow quickly and enter the ocean as smolts in March, a month or more before the river-type. This is a huge advantage for the estuary-type. The hatchery programs could focus more effort on this type by out-planting fry to the estuary or lower river floodplains immediately above the estuary (e.g., Yolo Bypass). Experimental out-planting of hatchery fry to rice fields in the Yolo Bypass has proven promising2. There are also many natural habitats in the lower river floodplains and Bay-Delta that could accommodate out-planting.

This post is part of a 4 part series on hatchery reform, check back into the California Fisheries Blog over the next week for Parts 3 and 4.

Drought Effect on the Bay

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During the past four years of drought little has been said about the specific effect of the drought on the Bay, especially the upper Bay. Suisun Bay is a very important part of the San Francisco Bay Estuary as it receives freshwater flow from the Delta and is the low salinity mixing zone of the Bay-Delta ecosystem. Suisun Bay is also critical habitat of many listed estuarine and anadromous fishes. The drought has brought something new: unprecedented high salinities to Suisun Bay from relaxed Bay-Delta Plan Delta outflow and salinity standards. In the chart below (Figure 1) salinity levels as measured by micro-mhos of electrical conductivity (EC) were high (>15,000 EC) at Port Chicago in west Suisun Bay in April and May 2014 and 2015. Normal dry year levels are shown by 2012, when the Delta Outflow standard is 7100 cfs and the Collinsville salinity standard is 2780 EC. In 2014 and 2015, the standards were relaxed to save reservoir storage. The Outflow standard was reduced to 4000 cfs. The salinity standard location was moved upstream into the Delta. Although unregulated flow dominated most of the Apr-May period in 2012 (Figure 2), the regular standards applied in the latter half of May.

Figure 1. Salinity (EC) in Suisun Bay in April-May 2012, 2014, and 2015.

Figure 1. Salinity (EC) in Suisun Bay in April-May 2012, 2014, and 2015.

The potential ramifications of these unprecedented low outflows and high salinities are wide ranging and substantial.

  1. Invasive species will increase their presence in the Bay-Delta. Clams, zooplankton, and fish communities will change. Invasive Potamocorbula clams abundance has likely increased and moved further upstream1. More clams mean less plankton and higher selenium concentrations in clams.

    “The biomass of the larger copepods is less than it was before the introduction of the clam Corbula amurensis, because of competition for food and grazing by clams on the early life stages of copepods. The resulting low abundance of copepods of suitable size, and the long food chain supporting them, may be contributing factors to the decline in abundance of several estuarine fish species.”2

    “Many scientists in the U.S. geological survey, who have been studying the Bay for decades, also concur with Strong, that the clam is likely the culprit”.3

  2. Young Longfin and Delta Smelt have been forced to rear in the Delta rather than the Suisun Bay. Mysid and Bay shrimp production will be lower.
  3. Concentration of contaminants will be higher in Suisun Bay, possibly leading to toxicity to plankton, benthic invertebrates, and fish.
  4. Unbalanced levels of ammonia, nitrogen, and phosphorous nutrients will lead to trophic changes in the plankton community (e.g. more blue green algae and lower diatom production).
  5. Less inflow to Suisun Bay means less organic carbon and other nutrients necessary to stimulate the estuary’s food chain. Turbidity from river sediment will be lower.

Less inflow to the Delta and less outflow to the Bay also mean more nutrients, plankton, and fish are drawn to the South Delta export pumps. Even with restricted pumping at 1500 cfs limit, the effect is proportional and significant. In reality, Delta outflows are lower than the NDOI estimates provided by DWR and Reclamation. A 14-day running average relaxed standard of 4000 cfs often leads to “real” outflows closer to zero4.

More on the effects of outflow on Suisun Bay can be found at:
http://www.sfestuary.org/wp-content/uploads/2015/03/Estuary-MAR2015-v8a-finalWEB.pdf .

Figure 2. Delta outflow (NDOI) in April-May 2012, 2014, and 2015.

Figure 2. Delta outflow (NDOI) in April-May 2012, 2014, and 2015.