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.

Sites Reservoir —
Potential Benefits for Fish,
Potential to Worsen Conditions for Fish
Working Presumption: Thumbs Down

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The proposed Sites Reservoir1 would be a new off-stream storage reservoir covering 12,000 -14,000 surface acres with 1.8 million acre-ft of storage capacity on the west side of the Sacramento Valley (Figure 1). The project would capture and store unregulated Sacramento River winter-spring runoff and some water previously stored in Shasta Reservoir. The diversion capacity to the reservoir would be 5400-6500 cfs, supplied by two existing river diversions (up to 1800 cfs at Red Bluff; up to 2100 cfs at Hamilton City) and a new diversion near Colusa (proponents are evaluating alternative capacities of 1500 and 3000 cfs, in addition to the currently preferred capacity of 2000 cfs). The Sites Authority webpage estimates that it could have diverted over 1 Million acre-ft to storage in Sites in 2018 and 1.8 Million acre-ft to storage in 2017; these figures assume bypass flow requirements at the diversion points and at Freeport, and sufficient storage capacity in the reservoir. The Draft Environmental Impact Report/Environmental Impact Statement (DEIR/DEIS) for the Sites Reservoir Project estimates the average annual diversion to Sites storage at about 500,000 acre-ft; actual diversions would vary depending on hydrology and regulatory constraints.

As an off-stream storage reservoir, Sites would store water behind a dam that is not on a major waterway. Water diverted to the reservoir would be pumped into canals from the Sacramento River, and then pumped into the storage reservoir from small holding reservoirs on the canals. The two existing diversions that would fill Sites have modern fish screening facilities. As currently envisioned, a pump-back hydroelectric operation would allow partial recovery of pumping costs.

The Sites project has potential benefits for fish, but also the potential to worsen conditions for fish.

Potential Benefits for Fish

  1. Under current operations, existing irrigation diversions on the Sacramento River draw water primarily in spring and summer via several major canal systems on the west side of the Sacramento Valley. These diversions draw mainly on water that was previously stored in Shasta Reservoir and released to the Sacramento River in part to keep river water temperatures cool. Shasta Reservoir’s cold-water pool varies in volume depending on storage and other factors, and can run out if it is not managed carefully. If the cold-water pool is depleted at the end of the summer, this threatens the viability of winter-run salmon. Under current operations, spring and summer irrigation diversions from the Sacramento River also cut flow and raise water temperatures in the lower river, which harms salmon, steelhead and sturgeon. Water diverted to storage in Sites in the winter could substitute for some of the spring and summer irrigation deliveries that currently come from Shasta. A greater percentage of water released from Shasta in spring and summer could then flow all the way to the Delta. More water could also be retained in Shasta Reservoir to protect the Shasta cold-water pool into the fall and as carryover for the following year.
  2. If more water were delivered to the Delta from Shasta Reservoir in the spring and summer, less water would theoretically be needed from Folsom and Oroville reservoirs to meet Delta water quality, outflow and other requirements. This could allow more targeted releases of water into the lower American and lower Feather rivers to protect fish in those waters. It could also allow better maintenance of cold-water pools and greater carryover storage in Folsom and Oroville, also very important for the respective fisheries downstream.
  3. Water stored in Sites could be delivered directly to the Delta via the Colusa Basin Drain (CBD) system and Yolo Bypass, reducing outflow demands from other Valley reservoirs. Water delivered directly to the Delta from Sites would be of higher potential productivity and could stimulate winter-spring Bay-Delta plankton blooms that would benefit Delta native fishes.

Potential to Worsen Conditions for Fish

  1. The proposal includes a new point of diversion on the Sacramento River with a capacity to divert 2000 cfs. This would give the project higher diversion capacity and the capability of diverting tributary runoff that would otherwise be unavailable to the two upper river diversions that now enters the Delta. This diversion would also affect flows and water temperatures in the lower Sacramento River, and subject migrating juvenile salmon, sturgeon, and steelhead to a third large screening facility. The new point of diversion would be particularly problematic if it diverted water outside the peak runoff season (late fall through spring).
  2. The new diversion and the reoperation of canal intakes at Red Bluff and Hamilton City to divert water in winter would compete for water with Delta diversions and would affect Delta outflow to the Bay.
  3. Water deliveries and hydropower releases from Sites Reservoir to the lower river at the new diversion site could affect water quality in the lower Sacramento River.
  4. With available winter off-stream storage, the existing diversions at Red Bluff and Hamilton City would be capable of diverting uncontrolled flows from tributaries that have otherwise remained relatively untouched down to the Delta.
  5. The greater diversion capacity may increase demands on Shasta storage and will increase diversion of uncontrolled tributary flows, further compromising fishes in the Sacramento River and the Bay-Delta.
  6. A small but potentially significant amount of water supply stored in Sites Reservoir would be lost to evaporation and groundwater seepage.

Above all, there is too much unknown to evaluate how Sites would affect fish.

As is the case for most proposed water supply projects, the project description in the draft DEIR/DEIS for Sites describes several potential configurations of project infrastructure and a description of proposed constraints. The DEIR/DEIS does not evaluate different constraints, such as different bypass flow requirements past each point of diversion; the DEIR/DEIS only evaluates one value for each point. In spite of numerous requests that the DEIR/DEIS evaluate project diversions with more stringent Delta flow and water quality requirements than the existing inadequate ones, the DEIR/DEIS only evaluates project yield with existing Delta constraints.

The benefit side is even more vague and conceptual. The entire construct of hypothetical Sites benefits would in fact require a new type of proscriptive rules and enforcement mechanisms that would be unprecedented for California water projects. There is simply no clue in any of the Sites literature what those rules would be or even could be.

The project description places no numbers on how much water stored in Sites the project’s operators would dedicate to actions designed to benefit fish. The project description defines no decision-making process for dedicating water to fish, other than to say that on an overarching basis fish agencies will decide. The project description defines no way in which project operators will apportion water for fish against water for water supply. For all the offsets that seem to comprise the lion’s share of fish benefits, the project description does not say how water from Sites will generate improvements in operation of state or federal reservoirs, or whether it will be Sites operators or state and federal operators who make the calls.

Then there is the question of whether there would be any offsets at all. There is no assurance that there will be any decreases at all in water use from Shasta or from other state and federal reservoirs. Water freed up by using Sites to meet Sacramento Valley water supply could simply allow Sac Valley water users to irrigate more land or sell more water for export at the Delta pumps. The DEIR/DEIS proposes no mechanism of enforcing offsets: who would regulate the project’s use of water, who would manage the interaction between Sites water and water from Shasta, Oroville, Folsom and perhaps Trinity reservoirs, and how and against whom any requirements would be enforced.

There are other problems. A shift to winter-spring diversions and use of canal systems would potentially change groundwater recharge and use patterns in the Sacramento Valley. The project would compete for water available to the proposed WaterFix Twin Tunnels project in the Delta. Sites and WaterFix have their “sights” on the heretofore untouched tributary inflows that are also protected by Delta export OMR limits so the flows reach the Bay. There will be a big fight over this uncontrolled water that now makes up a significant portion of the Bay’s freshwater input in drier years. Both projects have claimed future benefits of the same pot of water.

Conclusion

There are potential benefits from Sites project’s main features to Central Valley fishes, including salmon, steelhead, sturgeon, smelt, and striped bass. Most of the benefits would result from switching the diversion time period of the two existing upper river diversions and Shasta reservoir releases to these diversions. The added new diversion and increase in winter diversions will at important times reduce Sacramento River flow and Bay-Delta inflow and outflow, harming fish in certain but sometimes hard to quantify amounts.

Past water developments in the Central Valley have overwhelmingly made conditions for fish worse. The Sites project proponents claim that their project will be different. These proponents have not done themselves, the public, or public policy any favors by relying on generalities and politics as the centerpieces of their efforts to advance their project. At this time, there are too many unknowns to meaningfully evaluate the possibility that benefits might outweigh the harm and justify the costs. In the meantime, it is a reasonable working presumption that the Sites project will worsen conditions for fish as well.

Figure 1. Proposed Sites Reservoir and associated infrastructure on west side of the Sacramento Valley.

More on the Winter-Run Salmon Decline

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In a March 14, 2018 post, I discussed my long-held theory that the winter-run salmon decline was caused in large part by high fall exports from the Delta that began in the mid 1970s. In this post, I add some further insights on the theory and why it is so important.

First, when the State Water Project came on line in the late 1960’s, potential export pumping more than tripled from 4,400 cfs to 15,000 cfs. In reality, increases in previously low federal fall exports, along with higher state exports, led to much sharper increases in fall exports, particularly in 1975, 77, 80, 82, and 84, coincident with the primary period of winter-run decline from 1975-85. The fall export increase is very evident in the federal export record (Figure 1) and state export record (Figure 2).

Second, the high exports and high salmon salvage observed were not always associated with high Delta inflows. High salvage of winter-run sized juvenile salmon at south Delta export intakes occurred at the end of October 1984 (Figure 3) under low Delta inflow/outflow conditions (Figure 4). This is important because DWR, in its assessment of the WaterFix Project, is maintaining that export restrictions during the first fall and winter flow pulses will be protective of migrating juvenile salmon. But pulse restrictions alone would not be protective.

WaterFix would nearly double the export capacity of the State Water Project. Actual fall exports could increase by 50%, with much of the increase coming from the trio of new North Delta Diversion tunnel intakes that lie directly in the migration path of young winter-run salmon.

Figure 1. Unusually high federal exports occurred in fall 1975, 1980, and 1984 (red circles).

Figure 2 Delta SWP exports in daily average cubic feet per second from 1969 through 1983.

Figure 3. Chinook salmon south Delta export intakes salvage in fall 1984.

Figure 4. Delta inflow from the Sacramento River August 1984 through March 1985.

And then there were none…

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ARE DELTA SMELT FINALLY EXTINCT? HAS THE CANARY SUNG ITS LAST SONG?

In late April and early May 2018, 20-mm Surveys collected no Delta smelt (Figure 1) in the San Francisco Bay-Delta estuary. It’s a new low for Delta smelt since the survey began in 1995, worse even than the 2017 survey catch (Figure 2). The outlook for the population as indexed by the summer and fall surveys looks grim after record lows from 2012-2017. Despite good conditions in spring 2018, the number of adult spawners was too low, indicating a weak recovery potential.

Figure 1. Catch and lengths of Delta smelt collected in the 20-mm Survey in spring 2018. None were collected in surveys 4 and 5

Figure 2. Catch and lengths of Delta smelt collected in the 20-mm Survey in spring 2017.

Pacific Herring and Bay Productivity

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In past posts I have focused on salmon, smelt, sturgeon, and striped bass, even zooplankton, but have yet to discuss Pacific herring. Pacific herring are the Bay-Delta estuary’s most abundant fish and like the other fishes previously mentioned also depend on the estuary for spawning, rearing, or migration. They also support an important commercial fishery in the Bay. 1

Herring larvae and juveniles are also important prey for young salmon and other estuarine and marine fish from winter into summer. Sub-adult and adult herring are key elements of the coastal marine food web of the northern Pacific, from California to Alaska. Herring populations of the northern Pacific, including the Bay’s population, have been generally managed by controlling harvests (usually with quotas or effort limits) and stock-fishery models.2 Like most fish stocks managed by harvest, the populations tend to become overfished with subsequent difficult recovery. The role of the environment in juvenile fish recruitment is often overlooked because it can be very complicated.

Unlike the freshwater spawning smelt, salmon, and sturgeon, herring spawn in coastal marine and estuarine bays including San Francisco Bay, and their larvae move upstream in winter with tidal and estuarine circulation into brackish waters to rear. Some larvae born in San Francisco Bay even drift with tides up into the Delta. Most rear in brackish waters of the North Bay (San Pablo and Suisun bays) feeding on estuarine plankton whose productivity is positively related to freshwater outflow from the Delta and coastal ocean upwelling (enhanced feeding from turbidity and nutrient driven plankton blooms3). When winter storms and associated pulses of freshwater into the Bay are generally common, Bay productivity in winter is generally dependable, as is herring production regardless of the water year type.

However, at some point herring and general Bay productivity will suffer (if not already) if larger portions of freshwater outflow to the Bay are stored in reservoirs or directly diverted for water supply, especially in drier water years. Proposed projects like California WaterFix (Delta Tunnels) and new storage reservoirs will do just that – take more of the water that would normally enter the Bay, especially in drier years with limited runoff to the Bay.

One potential clue about herring productivity is density patterns of larval herring in the winter during peak abundance. Figures 1-4 show February herring densities versus salinity concentration in four recent years of the Smelt Larval Survey. Figure 5 shows long-term trend in Pacific herring densities in April Bay midwater trawl survey. Taking into account biased-low catch in very wet years (1983, 1995, 1996, 1998, 1999), there is a clear downward trend, with very low catch in 2015-2016. With limited data like this it is hard to see real abundance patterns let alone factors that have led to observed differences. There are so many important factors acting together and independently, it is (and will) be hard to determine cause and effect.

Is the pattern in Figures 1-5 a start of a trend of lower densities and more near zero densities in certain areas of the estuary? More analyses and synthesis are needed to answer the question. More science in the form of studies and comprehensive surveys is needed if we are to understand the role of freshwater outflow to the Bay and coastal waters. Is freshwater outflow to the Bay being “wasted” at the expense of human endeavors, or is it a critical element of the coastal ecosystem productivity? I would guess the latter. Pacific herring would be a good ecological indicator or canary in the coal mine, as Delta smelt once were.

Figure 1. Density of Pacific herring in larval surveys of the Bay-Delta versus surface salinity in February 2011, a wet water year.

Figure 2. Density of Pacific herring in larval surveys of the Bay-Delta versus surface salinity in February 2012, a below normal water year.

Figure 3. Density of Pacific herring in larval surveys of the Bay-Delta versus surface salinity in February 2014, a critically dry water year.

Figure 4. Density of Pacific herring in larval surveys of the Bay-Delta versus surface salinity in February 2018, a below normal water year.

Figure 5. Long term trend in Pacific herring average April catch per trawl in stations 100-500s in Bay in Bay midwater trawl survey.

Spring 2018 – Unusual at Best

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Flow conditions into and through the Delta are creating an unintended adaptive management experiment this spring. The San Joaquin River is providing half of the 20,000 cfs of Delta inflow. Exports and other water diversions are each taking about 3000 cfs from the Delta, leaving 14,000 cfs for outflow to the Bay. The Delta has been free of salt (Collinsville has been fresh at 200 EC, but salt is now encroaching). These are good conditions for the Delta and the San Joaquin, but horrendous for the Sacramento. Such conditions are highly unusual.

The Bureau of Reclamation’s decision to save water in Shasta reservoir, combined with a low water level in Oroville Reservoir because of ongoing repairs, have led to poor flows and high water temperatures in the lower Sacramento River. Flow at Wilkins Slough on the Sacramento River above Feather River confluence has fallen to 4000 cfs (Figure 1). Flow in the Sacramento River at Verona, below Feather River confluence, is only 7000 cfs (Figure 2). Water temperatures have reached 60°F at Red Bluff and 70°F at Wilkins Slough. Water temperatures above 56°F are detrimental to spawning winter-run salmon near Red Bluff. Water temperatures above 65°F are detrimental to out-migrating juvenile salmon, steelhead, and sturgeon.

A recent increase in releases from Shasta Reservoir is accommodating agricultural diversion demand in the upper Sacramento River below Shasta (Figure 3), while flows decline in the lower river. The increase in the upper river has stimulated emigration of wild juvenile salmon from the upper river, as shown by increased catch at the Red Bluff screw traps (Figure 4). The problem is that two-thirds of river flow is being diverted for Sacramento Valley agriculture, and river temperature rises 10°F along the way. Sacramento River salmon that reach the Delta, along with other Central Valley wild and hatchery salmon, are subject to south Delta exports (Figures 5 and 6). Though south Delta exports have been reduced, their effect remains significant because of low Sacramento River inflow to the Delta.

As I have suggested in past posts, Shasta Reservoir releases should be increased or water diversions from the upper Sacramento River reduced by several thousand cfs, in order to increase lower river flows and reduce water temperatures to no higher than the state water quality standard of 68°F. If this action is not taken, we will simply be feeding most of the young salmon to the abundant stripers that thrive in warm water conditions between Redding and the Bay (Figure 7).

Figure 1. Sacramento River flow at Wilkins Slough in spring 2018.

Figure 2. Sacramento River flow at Verona in spring 2018.

Figure 3. Sacramento River flow below Shasta/Keswick dams in spring 2018.

Figure 4. Catch of juvenile salmon in screw traps, water temperature, river flow, and turbidity near Red Bluff in Sacramento River.

Figure 5. Juvenile Chinook salmon salvage at south Delta export facilities in spring 2018. Red circle outlines recent salvage of wild juvenile spring- and fall-run smolts.

Figure 6. Juvenile Chinook salmon salvage at south Delta export facilities in spring 2018.

Figure 7. Striper limits from late April 2018 guide trip on lower Sacramento River. Source: James Stone.