Category Archives: Bay-Delta

Delta Smelt Summer 2016 Update

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Past summer surveys in the Cache Slough, Liberty Island, and Deepwater Ship Channel areas of the northern Delta frequently collected Delta smelt. Some documents even referred to this area as the last refuge of Delta smelt.

“The southern end of the Yolo Bypass, including Liberty Island (Table 9-2), Cache Slough, and the DWSC are known to support Delta Smelt spawning and rearing (Bennett 2005) (Grimaldo et al. 2004). The USFWS found Delta Smelt in shallow water habitats within Liberty Island using a variety of fish sampling techniques (Figure 9-1). Delta Smelt catch and gonadal staging from fish collected from the Spring Kodiak Trawl (SKT) surveys also indicate that the DWSC is an important spawning location in the Delta (Figure 9-2). Additionally, a non-migratory contingent has been recently observed to remain in freshwater and carry out their entire lifecycle in the tidal freshwater region of the CSC, which offers cool, turbid habitat and abundant prey (Sommer et al. 2011). DWR 2015 1

Surveys picked up some Delta smelt in the northern Delta even in the 2012-2015 drought years. In fact, most of the few smelt detected in those years came from this area.

However, the 2016 Summer Townet surveys caught no smelt in the northern Delta’s Cache Slough area at all. The extreme water temperature conditions present in 2012-2015 (August water temperatures in the 23-26°C range, near lethal to smelt) occurred again this summer (see chart below).

One Delta smelt was caught this summer downstream of the Delta, in Grizzly Bay at the mouth of Montezuma Slough.  There is at least one Delta smelt left.  Hopefully, the Fall Trawl Survey will collect a few more.

Water temperature (°C) in lower Yolo Bypass Tule Canal (green) and adjacent Deepwater Ship Channel (blue) in July 2016. (USGS data)

Water temperature (°C) in lower Yolo Bypass Tule Canal (green) and adjacent Deepwater Ship Channel (blue) in July 2016. (USGS data)

  1.  Draft FRP Cache Slough Complex Conservation Assessment, p. 9-2, http://www.water.ca.gov/environmentalservices/cache_slough_assessment.cfm  ↩

Summer 2016 Delta Salinity and Outflow Standards

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The present water quality standards for the Delta were established by the State Water Resources Control Board in 1995. The standards govern how the Delta water projects operate and indirectly control much of the Central Valley’s water management. The standards also have a substantial influence on the ecosystem health of river, the Delta, and the Bay . These standards have been under review for a decade and are badly in need of update and revision. These standards have been responsible for the decline of Central Valley native fishes, including the listing of six under state and federal endangered species acts.

In this post, I discuss the Delta standards relative to performance in summer 2016, the first near normal water year (at least for the Sacramento River watershed) after four years of drought.

The summer Delta standards govern Delta salinity, Delta outflow, Sacramento River flow at Rio Vista, and south Delta export limits. Of the four, salinity and outflow governed the Delta in summer 2016, with river flow and exports (percent of inflow) well within prescribed limits.

The salinity and outflow standards are monthly average limits (objectives). Monthly average standards of salinity are prescribed as electrical conductivity at Emmaton and Jersey Point in the west Delta (Figure 1), as well as other locations in the interior and south Delta.

The problem is that these standards are specifically designed to protect Delta agriculture and export water quality, not Delta ecology or its native fishes. That specific deficiency is what caused federal biological opinions to add restrictions to limit south Delta exports; however, none of these applied in summer 2016. Although the agricultural standards do provide some ecological protection, the specific hydrology shown in Figure 1 results in brackish water being drawn into the central and south Delta, which degrades the low salinity zone that is so critical to the Bay-Delta native fishes.

Figure 1. Western Delta salinity and flow monitoring stations. Blue arrow denotes primary source of fresh water input to Delta from the Sacramento River. Red arrows indicate net negative flows from west Delta toward south Delta export pumps in summer 2016. Under these conditions Jersey Point salinity tends to be controlling.

Figure 1. Western Delta salinity and flow monitoring stations. Blue arrow denotes primary source of fresh water input to Delta from the Sacramento River. Red arrows indicate net negative flows from west Delta toward south Delta export pumps in summer 2016. Under these conditions Jersey Point salinity tends to be controlling.

Delta Inflow

Approximately 4 million acre-feet (maf) of water entered the Delta from the Sacramento River in summer 2016, primarily from reservoir releases to satisfy agricultural demands and meet salinity/outflow standards. The 4 maf of Sacramento River inflow to the Delta represented approximately 90% of total Delta inflow. The remainder came from limited San Joaquin flow. and other sources.

Figure 2. Delta inflow from the Sacramento River in summer 2016.

Figure 2. Delta inflow from the Sacramento River in summer 2016.

Delta Outflow and Diversions

Of the approximately 4.4 maf of total Delta inflow in summer 2016 (Figure 3), only 1.8 maf (40%) reached the Bay. Total exports and diversions from the Delta were 2.6 maf (60% of total inflow). Delta outflow standards controlled until mid-July when salinity standards took control. The additional outflow for salinity control above that necessary to meet outflow standards was provided primarily by reducing south Delta exports by approximately 300,000 acre-ft because of limited available upstream reservoir storage.

Figure 3. Delta outflow in summer 2016. Red lines denote Delta outflow standards for a Below Normal water year. Higher outflows than prescribed after mid-July were required to meet salinity standards.

Figure 3. Delta outflow in summer 2016. Red lines denote Delta outflow standards for a Below Normal water year. Higher outflows than prescribed after mid-July were required to meet salinity standards.

Salinity

Salinity standards took control in July (Figure 4) as Delta outflow failed to keep brackish water from the Bay from encroaching up the San Joaquin channel to Jersey Point. After mid-August salinity standards for the south Delta (700-1000 EC limits) became controlling (Figure 5).

The Problem and Solution

Too much salt is allowed into the interior Delta in summer, resulting in the degradation of water quality of diversions/exports and of the low salinity zone habitat of native estuarine fishes, including Delta smelt.

The solution is to extend the early summer 450 EC standard at Jersey Point (Figure 4) through the summer in abundant water years where high exports are planned from the south Delta. In low water supply years when exports are curtailed due to limited reservoir storage, a less stringent standard can be applied. In addition, in drier years, barriers can be placed on False River and Dutch Slough to limit movement of brackish water (and low-salinity-zone fish and their food supply) into the interior Delta.

Figure 4. Salinity (EC) at Jersey Point in the San Joaquin channel of the west Delta in summer 2016. Red lines denote salinity standards applicable at Jersey Point in summer 2016.

Figure 4. Salinity (EC) at Jersey Point in the San Joaquin channel of the west Delta in summer 2016. Red lines denote salinity standards applicable at Jersey Point in summer 2016.

Figure 5. Salinity (EC) in Old River in south Delta in summer 2016. Red lines denote 30-day running average salinity standards applicable to south Delta.

Figure 5. Salinity (EC) in Old River in south Delta in summer 2016. Red lines denote 30-day running average salinity standards applicable to south Delta.

Predation

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“While state and federal wildlife agencies, university researchers, and water users all agree that predation from non-native fishes is a major stressor on salmon populations, we have done nothing to try to directly curb its impact.”

This statement in a recent Fishbio blog post is simply not true.

In 1995, the state removed limits on summer Delta exports that had been in place for decades to protect young striped bass. Stocking of striped bass ended at the beginning of this century. Both actions contributed to record low production of striped bass over the past decade. 1 The Bay-Delta population of striped bass is now greatly depressed. The river population is sustained by the continuing policy of releasing hatchery salmon smolts in the spring at the hatcheries, an unnatural process that simply feeds the river stripers.2

The real problem is spring water management in the Sacramento and San Joaquin rivers that brings unnaturally low flows and warm, clear water that favors the predators. All the salmon runs naturally have juveniles migrating to the Bay in high cold flows from late fall to early spring when predators are inactive and ineffective. But with dams holding the water from winter rains and snows, the rivers lack natural winter flows and spring snowmelt.

Largemouth bass production in the Delta has increased because of habitat changes from water management, droughts, and invasive aquatic plants that have turned the Delta into an “Arkansas lake.” Smallmouth bass production has increased in the rivers with lower, warmer flow conditions from spring through fall.3

The native pikeminnow also benefit from the habitat changes in the rivers and Delta, as well as the abundance of spring hatchery smolts. Huge schools migrate from the Delta into the rivers in spring and summer to spawn. The tailwaters downstream of dams favor pikeminnow. The adults feed on young salmonids and the juveniles compete with juvenile salmonids. Juvenile pikeminnow that return to the Delta feed on smelt.

It is these habitat changes that have resulted in more effective predation on native salmon, steelhead, and smelts. Ignoring the cause won’t solve the problem. Focusing on the predators will not work. The basses and native pikeminnow have prolific reproductive systems. Killing more of them by removing regulations on their harvest or even putting bounties on them (like pikeminnow on the Columbia River) will not solve the root problem – habitat change. And without the predators, what would be left to control all the non-native forage and “trash-fish” that already plague the Delta and rivers?

In the future, if we continue to take more of the river flows and further degrade habitats, there will always be the temptation and the drumbeat to directly remove predators or inhibit their migrations. We can stop salvaging millions of these predators every year at the South Delta export facilities, stop returning all the bass caught in fishing tournaments, and truck all the remaining salmon produced only in hatcheries to the Bay. In the end we will still have abundant predators, an “Arkansas-like lake,” hatchery salmon, and at best novelty populations of endangered wild salmon, steelhead, sturgeon, smelts, complemented by likely newly listed species of native fishes like splittail, blackfish, hitch, etc.

Smallmouth Bass Expansion (Hypothesized)

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One of the major salmon predators on the Columbia River is the smallmouth bass. Long protected because of its contribution to a highly popular sport fishery, that protection is now gone because of the predation threat to Columbia River salmon recovery. Smallmouth and walleye are highly regarded game fish, but are not native to the Columbia River. They compete with and prey upon salmon. The Columbia states recognized this and no longer regulate these fisheries. This change will help prevent expansion of these species as global warming provides more favorable conditions for these cool-water non-natives than for the cold-water salmon, sturgeon, and steelhead.

Smallmouth bass have long been present in the Central Valley, especially in the lower Sacramento River and the rim dam reservoirs. Recent changes in the management of water in the lower Sacramento River will accelerate expansion of smallmouth and their preferred habitats over that of global warming alone. Smallmouth have historically been constrained by Basin Plan’s 56°F water temperature limit at Hamilton City (or Red Bluff) and the 68°F limit below Hamilton City to the Delta. However, smallmouth are highly likely to expand their population and range in the lower Sacramento River due to recent changes in flow management strategies that provide lower flows, warmer waters, and less turbidity to nearly 200 miles of the lower Sacramento River.

Ironically, the strategy changes meant to save water and cold-water reservoir supplies for salmon will actually benefit smallmouth, a key predator on salmon. The changes have already benefitted striped bass by enhancing their opportunities for predation. 1 An expansion of the smallmouth population is now likely because of warmer spring water temperatures (Figures 1 and 2) caused by lower river flows in the spring (Figure 3). The more days water temperatures exceed 60°F, the more successful spring breeding and survival of smallmouth will be. 2

Removing fishery protections will not solve the potential population enhancement or predation problems of smallmouth in the Central Valley. It would be a purely symbolic measure because smallmouth are so abundant and widely distributed. It is limitations on their habitat that have held back their expansion and the impact of their predation on salmonids. With the habitat limitations lessening, the smallmouth population will expand and contribute more to the predation problem. The solution is to restore former habitat limitation on smallmouth by sticking to the Basin Plan standards.

For more on smallmouth life history see this excellent YouTube video: https://www.youtube.com/watch?v=hoZ81au_YZg. Note in the video the strategy of smallmouth feeding heavily in the fall on small fish to store energy for the coming winter. Fall is when the winter-run salmon juveniles produced over the summer start their 200-mile downstream journey from the upper river spawning grounds to the Bay. All 200 miles have smallmouth bass.

Figure 1. Water temperature in Sacramento River at Red Bluff (RM 243) in spring 2016. Red line depicts Basin Plan limit of 56°F for river at Red Bluff.

Figure 1. Water temperature in Sacramento River at Red Bluff (RM 243) in spring 2016. Red line depicts Basin Plan limit of 56°F for river at Red Bluff.

Figure 2. Water temperature in Sacramento River at Wilkins Slough (RM 125) in spring 2016. Red line depicts Basin Plan limit of 68°F for lower river.

Figure 2. Water temperature in Sacramento River at Wilkins Slough (RM 125) in spring 2016. Red line depicts Basin Plan limit of 68°F for lower river.

Figure 3. Sacramento River daily flow for years 2008 to June 2016. Red line depicts normal flow of 5000 cfs. Circles depict the tendencies for lower flows in recent years including spring 2016.

Figure 3. Sacramento River daily flow for years 2008 to June 2016. Red line depicts normal flow of 5000 cfs. Circles depict the tendencies for lower flows in recent years including spring 2016.

My comments on: “SLDMWA Response to Environmentalists’ August 9, 2016 Request to the SWRCB for Even More Water Aimed at Protecting Delta Smelt”

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On August 11, Jason Peltier, executive director of the San Luis-Delta Mendota Water Authority, offered comments on a letter from environmental groups to the State Board that requested more water for Delta Smelt. Below, I provide some of Mr. Peltier’s statements, and a response to each:

1. “As environmental special interests request the State Water Resources Control Board expand failed policies on Delta Smelt, Californians are calling on the Board to implement new science-based, common sense approaches to protect the species. It is disheartening to see once credible environmental organizations calling for a “more of the same” approach – one that has so miserably failed for a quarter century – in a misguided attempt to help the imperiled delta smelt.”


Comment: The environmental organizations were proposing what the state has also offered as its new strategy for the Delta Smelt. It is not the old misguided “failed” strategy of diverting more and more water and providing less and less Delta outflow to the Bay. The state’s new strategy derives from some of the same actions suggested in this past April’s science workshop on Delta Smelt held at UC Davis, which Mr. Peltier attended.

2. “[t]he Projects have compensated for Mother Nature’s stinginess with water released from reservoirs, making the Delta far fresher than it would have been naturally.”

Fact: Just the “natural” summer inflow to Shasta Reservoir in the past four years of drought nearly equaled the amount allocated for summer Delta outflow. If you add up all the Central Valley’s “natural” inflow it would far exceed the Delta outflow allotted, even without accounting for use above the rim reservoirs.

3. “This dedication of water for fish from what was stored for drought relief has resulted in unprecedented socio-economic and environmental harms to towns, farms, and numerous species living in the largest wetlands in the West.”

Fact: Most of the water stored is for agriculture and released for agriculture. Mr. Peltier’s organization is simply last in line for stored water and thus gets less water allocated during droughts. In June and July, nearly 30,000 cfs of water was released on average from Central Valley reservoirs, but only 7000-8000 cfs reached the Bay to repel salt intrusion. Because Shasta releases were reduced to protect salmon (not smelt), Mr. Peltier’s organization was unable to receive more than a minimal allocation. Again, this is because its water rights are junior to those of other users, not because of water allocated to smelt (none).

4. “Since the most severe cuts were imposed on the Projects nine years ago, less water has been diverted, and thus more Projects’ water has gone out to the ocean, than at any other time in the past 35 years.”

Fact: Seven of the last nine years were drought years. The only water consistently reaching the ocean in large amounts during those seven years was uncontrolled river flows and reservoir spills during and after sporadic winter storms. The only reservoir water that reached the ocean (Bay) in those seven dry years was the water necessary to hold back salt intrusion into the Delta so Delta diversions and exports remained possible.

5. “Farmers, fishermen, and environmentalists – everyone that truly cares about the status of our imperiled fisheries – should be furious.”

Comment: The fishermen and environmentalists are “furious” because of government mismanagement of the Shasta Reservoir cold water pool that has nearly wiped out the Sacramento salmon runs, and because of the weakening of Delta water quality standards in 2014 and 2015 that allowed excess salt into the Delta and just about exterminated the Delta smelt population.

6. “Decades old state and federal policies have failed and brought delta smelt and salmon to the brink of extinction. The last thing we need is more of the same.”

Comment: Yes, decades-old policies of increasing exports from the Delta has brought near-extinctions. It started with the massive State Water Project that came on line in the 1970’s. Yes, the last thing we need is “more of the same” – increasing exports promised with the WaterFix.

7. “Like delta smelt, we need shelter, we need food, and we need safety from predators, toxics, and invasion. The state and federal regulatory agencies have ignored for far too long the full needs of delta smelt, only willing to do what is easy, and we have all suffered for it.”

Fact: Delta smelt need the cool, brackish, wind-blown turbid waters of Suisun Bay provided when Delta outflow is sufficient to keep the low salinity zone out of the warm, confined channels of the Delta and away from its massive export pumps.

8. “We can continue to ignore decades of sound scientific advice, or we can embark on a bold new initiative, one that is transparent and inclusive of stakeholders working with state and federal agencies to save delta smelt.”

Comment: We have ignored the scientific advice. It has always been there. What “bold new initiative?”

9. “Now is not the time for desperate action, it is the time for thoughtful action.”

Fact: Giving the Delta Smelt 1000 or 2000 cfs in June and July this year – instead of nothing (Delta outflow was allocated to repel salt) – would entail only 3-6% of the water released from reservoirs and 5-10% of Delta inflow. After all, the Delta Reform Act of 2009 mandates that the state must implement the “co-equal” goals of providing a reliable water supply and protecting, restoring and enhancing the Delta ecosystem.