Analyzing Fish Population Dynamics in the Bay-Delta

I have been analyzing the declines in Bay-Delta and Central Valley fish populations for over 40 years. Fish population dynamics were the focus of my college education and my 50-year career in environmental impact assessment. I have participated in all the major efforts to understand the Bay-Delta fish population declines. From all of these efforts, it is clear to me what has caused the major fish population crashes.


First and foremost are the well known historic factors, the original sins pre-1970s of diverting water, building levees and dams, urban development, gold mining, cutting forests, polluting rivers, over-fishing, and introducing non-native species. These explain many of the major native fish population declines and extinctions such as the Sacramento perch and San Joaquin spring-run Chinook salmon, and the near extinctions of Delta smelt, green sturgeon, winter-run and spring-run salmon, and steelhead.


Since 1970, there have been dramatic declines in salmon, steelhead, smelt, sturgeon, splittail, and striped bass, often described as “recruitment failure” or failure to reproduce. While some of the blame most certainly is on continuing effects of the aforementioned original sins, the major post-1970 shifts were the consequence of a new array of stresses that hit the whole fish community, especially native fish populations. Most certainly the droughts of 76-77, 87-92, 01-02, 07-09, and 12-15 were a major underlying factor; however, it was the man-made responses to the droughts that caused most of the damage. Asian clam and other non-native aquatic invertebrate invasions to the Bay-Delta in the 80s were another stress, in part brought on by the aforementioned factors. Poor water management response to these new threats has caused further damage. The big culprits of change were the water management stresses described below.

1. State Water Project

The addition of the State Water Project (SWP) in the mid-1970s nearly tripled Delta export capacity (4400 to 11,400 cfs pumping rate1) and annual exports (2 million acre-feet to 6 million acre-feet annual exports). The additional Delta exports had huge fish population effects in the mid-70s from salvage mortality and entrainment of young fishes, as well as on fish habitat conditions in the rivers, Delta, and Bay. These stresses resulted in major population declines, which in turn resulted in the imposition of export restrictions in new water quality standards in 1978 (D-1485), and eventually to species listings under the Endangered Species Act in the 1990s.

2. Reservoir Operations

The increase in exports changed reservoir operations, including within-year reservoir release strategies and long-term multiyear reservoir storage patterns. Reservoir storage was depleted faster in droughts because of higher water supply demands. These effects continue today.

3. Water Supply Demands

Ever-increasing water supply demands from agricultural and municipal users have reduced river flows, Delta outflow, and reservoir storage. It’s not only the Delta’s 6 million acre-feet of exports, but the more than 20 million acre-feet from other Central Valley water diversions.

4. Invasive Species

Invasions of non-native clams, shrimp, fish, and zooplankton species since the 1970s have occurred in-part due to changes in Bay-Delta hydrology and water quality, as well as physical and biological habitat conditions. Delta pelagic (open water) habitat is now dominated by low-productivity reservoir water. The low salinity or mixing zone of the estuary became far less productive because of species invasions and reservoir water moving through to the south Delta export facilities, taking productive low-salinity habitat with it. The Delta is warmer from higher warm river inflows from spring through fall to feed water project exports, further favoring non-native warm-water fishes. Turbidity is lower, favoring non-natives. Invasive aquatic vegetation benefits from low turbidity, and the vegetation further favors non-native fishes over native fishes.


Since 1990, there have been steps backward that have undermined effective strategies and actions that had been undertaken beginning in the late 1970s to help depressed fish populations. Below are five examples in a long list of actions/changes.

1. Changes to D-1485

Beginning In 1978, Delta water quality standards in Decision 1485 placed restrictions on Delta exports, improved Delta outflows, and set salinity standards that had benefits for native fishes. Beginning in the 1990s, these post-1970 constraints on water diversions were changed, ignored, or eliminated. For example, new standards in D-1641 (1995 Accord) dropped the D-1485 June-July export restrictions.

2. Eliminating VAMP Export Restrictions and Higher Outflow Requirements in April and May

The Vernalis Adaptive Management Plan (VAMP) from 2000-2009, and its operational precursors under the CVPIA (1991) and the 1995 Accord, sought to protect Central Valley salmon and Delta native fishes by reducing April-May Delta exports and increasing spring Delta inflows and outflows. During the VAMP years, exports were restricted to less than 2000 cfs in April-May to protect fish (Figure 1). In the post-VAMP decade, restrictions were lifted and exports increased, especially in post-drought recovery wet years 2011 and 2017 (Figure 2).

3. Temporary Urgency Change Petitions (TUCPs) and Orders

Temporary urgency change orders during the recent drought allowed April-May Delta outflow to fall to around 5000 cfs in 2014 and 2015, from the normal near-10,000 cfs lower limit (Figure 3). Such low outflows in combination with Delta exports are devastating to Delta native fishes and Central Valley salmon and steelhead.

4. Delta Channel Barriers

The operation of the Delta Cross Channel, Head of Old River, South Delta, and False River barriers helps to keep export salinity down by funneling the fresher Sacramento River water to the south Delta export pumps. This increases the efficiency of exports in taking reservoir water in drier years and seasons. With the exception of the Head of Old River, barrier operation also funnels Delta native fish production (pelagic eggs and juveniles) and migrating young salmon (and their low salinity habitat and food sources) directly to the export pumps instead of to the Bay.

5. Suisun Marsh Salinity Control Gates

Since the installation of the Suisun Marsh Salinity Control Gates (SMSCG) in Montezuma Slough in 1989, the Slough and Marsh no longer function as critical low salinity habitat in drier years and seasons. Without high freshwater inflow, the Slough and Marsh no longer maintain the high biological production the once contributed to the Bay. The following excerpt from a DWR 2019 blog post inadvertently describes how limited the benefits of Suisun Marsh have become in the absence of flow:

DWR launched a pilot project last year that directed more fresh water flow into Suisun Marsh. The action involved opening salinity control gates in the summer months instead of during fall and winter, as is customarily done to reduce salinity in the marsh for migrating ducks and other waterfowl. The Delta smelt relies on low-salinity water – opening the salinity control gates allowed the smelt to enter the marsh from the Sacramento River, where it can access greater amounts of food and shelter.

Extinction looms so closely over the Delta smelt population that the project could have been considered a success even if it didn’t lure any countable Delta smelt to the marsh, said DWR Lead Scientist Ted Sommer. Just creating the conditions that allow smelt to thrive – that is, low salinity levels, lots of food, and high turbidity or muddy water that magnetizes smelt – would have been a cause for celebration.


There are many, many other examples of adverse changes that have put fish population dynamics in the Delta in a perpetual downward spiral. Since 1970, almost of all them involve reduction of Delta inflow and outflow, elimination of measures to mitigate the effects of reduced Delta inflow and outflow, and/or the biological response to reduced Delta inflow and outflow.

Figure 1. State south Delta exports (Harvey Banks pumping plant) in spring 1997-2010.

Figure 2. State south Delta exports (Harvey Banks pumping plant) in spring 2011-2019.

Figure 3. Delta outflow April-May 2007-2009 and 2013-2015 droughts.




  1. Initially exports were even higher with the new 11,000 cfs export capacity of the State Water Project. Total exports reached 12,000-14,000 cfs

Would WaterFix Tunnel Intakes be Protective of North Delta Fish? You Judge!

The Department of Water Resources’ consultant on in the WaterFix tunnels hearing testified:

“But for those Smelts that are occurring in that area, the North Delta diversions will be designed to fish agency protective standards”… “That opening, based on analyses, would prevent entrainment of Smelts that are greater than about 21 to 22 millimeters.”1

“In the EIR/EIS, the only significant and unavoidable impact that we found was for Striped Bass and American Shad. This is because of entrainment of early life stages at the North Delta diversions. These are species that spawn upstream of the North Delta diversions, in large part…..2

For American Shad, studies suggest that many American Shad were upstream of the Delta and, therefore, when they’re coming down into the Delta, they would be sufficiently large to be screened by the North Delta diversions.”

Delta Smelt

Delta smelt spawn in the north Delta in late winter and early spring. Their juveniles occur through summer. Their young would be highly susceptible to entrainment throughout spring (Figure 1).

White Sturgeon

Sturgeon, both green and white, spawn above the Delta in the lower Sacramento River in early spring. Their larvae and early juvenile stages reach the Delta in spring at a size highly vulnerable to entrainment (Figure 2).

American Shad

American shad spawn in the lower Sacramento River and tributaries in late spring and summer. Their larvae and early juveniles are prevalent in the north Delta in late spring and would be highly vulnerable to entrainment (Figure 3).

Striped Bass

Striped bass spawn predominantly in the lower Sacramento River in spring. Their larvae reach the north Delta in May and June, and would be highly vulnerable to entrainment (Figure 4).


Splittail spawn in the lower Sacramento River floodplain in spring. Their early juveniles reach the north Delta usually in May and would be highly vulnerable to entrainment (Figure 5).

Prickly Sculpin

Prickly sculpin, an abundant native Delta fish, spawn in the lower Sacramento River in late winter and their larvae are found in the north Delta in early spring and would be highly vulnerable to entrainment (Figure 6).

Sacramento Sucker

Sacramento sucker spawn in Valley rivers in spring. Their larvae and early juveniles are present in the north Delta throughout spring and would be highly vulnerable to entrainment (Figure 7).

Threadfin Shad

Non-native threadfin shad, the most abundant forage fish in the Delta, spawn from late spring into summer throughout the Delta and lower rivers. Their larvae and early juveniles are prevalent in the north Delta in late spring and early summer, and would be highly vulnerable to entrainment (Figure 8).

Summary and Conclusions

Larval and early juvenile lifestages of many Delta fishes would be highly vulnerable to entrainment through the screens of the proposed WaterFix north Delta intakes. Juvenile/fry of these and other species (salmon3) would be highly vulnerable to impingement and predation at the screens.

Figure 1. Length frequency of Delta smelt captured in the California Department Fish and Wildlife’s annual Delta-wide 20-mm Survey. For each sub-graph within this figure and each of the following figures, the x-axis shows the length in millimeters of captured fish, and y-axis shows the number of captured fish of each length. Note that most of the early spring post-spawn larvae and juveniles are of a size highly vulnerable to entrainment (<20 mm).

Figure 2. Length frequency of white sturgeon captured in the 20-mm Survey . Note larval sturgeon were captured soon after their spawning period in spring at a highly vulnerable size to entrainment. Many larvae of the main lower Sacramento River population of white sturgeon would pass the proposed WaterFix intakes.

Figure 3. Length frequency of American shad captured in the 20-mm Survey . Note that most of the shad would have to pass the proposed north Delta intakes in spring at a size highly vulnerable to entrainment (<20 mm).

Figure 4. Length frequency of striped bass captured in the 20-mm Survey . Note that most of these striped bass larvae would have had to pass the area of the proposed north Delta WaterFix intakes at a size would be highly vulnerable to entrainment (<20 mm).

Figure 5. Length frequency of splittail captured in the 20-mm Survey Note that many splittail spawn in the Sacramento Valley floodplain just upstream of the proposed north Delta WaterFix intakes, and that many of the juvenile splittail emigrating back to the Delta would pass the proposed WaterFix intakes at a size vulnerable to entrainment (<20 mm).

Figure 6. Length frequency of prickly sculpin captured in the 20-mm Survey . Note that the larvae of winter-spring spawning sculpin would be highly vulnerable to entrainment (<20 mm).

Figure 7. Length frequency of native Sacramento sucker captured in the 20-mm Survey . Note that the juveniles of late winter-early spring river spawning suckers return to the Delta at a size vulnerable to entrainment (<20 mm).

Figure 8. Length frequency of threadfin shad captured in the 20-mm Survey . Note the late spring-early summer spawning threadfin shad are highly vulnerable to entrainment (<20 mm).

  1. WaterFix hearing transcript, 2/23/18, Page 124, line 2:  Dr. Greenwood testimony at State Board WaterFix hearing.
  2. Id., Page 156, line 6.  Note that many shad and striped bass spawn their buoyant eggs in the area of the proposed intakes and immediately upstream, as well as in the lower Feather, Sacramento, and American rivers.  Nearly all the eggs and newly hatched larvae would pass the proposed CWF intakes.
  3. Much of the wild salmon production from the American and Feather rivers’ fall-run populations comes from fry (30-50 mm) leaving these rivers in winter.  Winter is the peak period of proposed north Delta diversions of the WaterFix project.  These fry would not be protected by the proposed WaterFix screens.

WaterFix will devastate more than just Salmon

Dave Vogel and I are contributing a series of posts on the potential effects of the WaterFix Twin Tunnels Project on Delta fishes. Our focus to date has been on salmon. In this post, I focus on the “other” fishes of the Bay-Delta that will be harmed by WaterFix.

Striped Bass (non-native gamefish)

Striped bass will be devastated by WaterFix tunnel intakes located on the lower Sacramento River. The main spawning run of striped bass is in spring in the lower Sacramento River from near Colusa down to the tidal Delta. Eggs and larvae are buoyant and are carried by currents to the tidal Delta and Bay. Nearly all the eggs and larvae must pass the tunnel intakes. The original Peripheral Canal (circa 1980) had a provision to limit diversions during the striped bass spring spawn. The Vernalis Adaptive Management Program (VAMP) from the late 1990s to the late 2000s protected striped bass in spring with higher Delta inflows and reduced exports (generally a limit of 1500 cfs from mid-April to mid-May). The D-1485 Delta standards had a limit on exports through June (6000 cfs). The proposed WaterFix would have spring exports up to 15,000 cfs (9000 from tunnels and 6000 from existing South Delta pumps). Those eggs and larvae that pass the tunnel intakes would be subject to the pull of south Delta exports without the benefit of the extra flow taken at the tunnel intakes.

Longfin Smelt (native)

Longfin smelt will suffer from reduced flows in the winters of drier years. The WaterFix will take a quarter to a third of sporadic uncontrolled winter flow pulses that support the spawn of longfin smelt in drier years. The lower flows will force longfin to spawn further upstream in the Delta where they are vulnerable to central and south Delta exports. The longfin population declines in drier year sequences; the WaterFix will add to downward population pressure.

Delta Smelt (native)

A recent post by Moyle and Hobbs at UC Davis suggests Delta smelt will be better off under WaterFix:

“The status quo is not sustainable; managing the Delta to optimize freshwater exports for agricultural and urban use while minimizing entrainment of delta smelt in diversions has not been an effective policy for either water users or fish.” Comment: So allowing the water projects to take more water will help? Delta inflow and outflow are the key factors in Delta smelt population dynamics – both will be negatively affected by WaterFix.

Moyle and Hobbes point out “reasons to be optimistic about Waterfix,” as follows:

  • “Entrainment of smelt into the export pumps in the south Delta should be reduced because intakes for the tunnels would be upstream (of) current habitat for delta smelt and would be screened if smelt should occur there.” Comment: The existing south Delta intakes will continue to take spring-summer water (and smelt) from the Delta in similar amounts as in the past. However, smelt in the south Delta will not have the benefit of the inflow taken by the proposed tunnels. Smelt will also be more likely to spawn near or upstream of the tunnel intakes. Screens on the tunnel intakes would not help save larval smelt and would be minimally effective for adult smelt.

  • “Flows should be managed to reduce the North-South cross-Delta movement of water to create a more East-West estuarine-like gradient of habitat, especially in the north Delta.” Comment: If outflow remains low or becomes even lower, the low salinity zone will more frequently move further into the Delta. The north Delta already has a strong gradient – allowing the gradient to move further upstream into the Delta will have adverse effects. Circulation in the south Delta will remain poor, and the south Delta will continue to experience reverse flows, because south Delta exports will continue. The south Delta will lose the benefit of inflow taken by the tunnels.

  • “Large investments should be made in habitat restoration projects (EcoRestore) to benefit native fishes, including delta smelt.” Comment: Delta smelt are totally dependent on pelagic (open-water) habitats, but few EcoRestore projects will improve such habitats. Salinity, water temperature, turbidity, tidal-flow dynamics, water quality, and nutrients are by far the most important factors controlling smelt population dynamics.

Steelhead (native)

Steelhead, much like salmon, are affected by ancillary changes in reservoir storage and releases, river flows, Delta inflow and outflow, water temperatures, and turbidities. But the greatest threat to steelhead, as for salmon, is from the three large intakes and their screen systems, which will adversely affect young steelhead passing on their way to the ocean.

Splittail (native)

Splittail were once on the endangered species list. Today, splittail numbers, especially for recruitment of juveniles, are way down, well below the numbers occurring at the time of their listing. Splittail from the Bay-Delta migrate upstream into river floodplains upstream of the Delta to spawn in spring. The three largest floodplain areas are in the Yolo Bypass, Sutter Bypass, and the lower San Joaquin River wildlife areas. The Sutter group will be at high risk to fry-stage entrainment/impingement at the tunnel intakes. The San Joaquin group will have a continued risk to south Delta exports, a risk made worse by the diversion of inflow from the Sacramento River into the tunnels.

American shad (non-native gamefish)

American shad migrate from the ocean to Valley rivers to spawn in the spring. Eggs, larvae, and fry from the major spawning rivers of the Sacramento Valley must pass the tunnel intakes in the north Delta. Like the striped bass, these lifestages of American shad will be devastated by entrainment and impingement at the tunnel intakes.

Pacific Lamprey

Like salmon and steelhead, Pacific lamprey migrate from the ocean to spawn in Valley rivers during the spring. Young larval lamprey would pass the tunnel intakes on their migration back to the ocean. Because they are weak swimmers they would be highly vulnerable to impingement or predation at the screens.

Native Minnows and Suckers

Many species of native minnows and suckers migrate upstream from the Delta to Valley rivers to spawn in spring and summer. Their young must pass the tunnel intakes on their return to the Delta, and thus will be at risk to entrainment/impingement at the tunnel screens.

The Delta smelt Summer Townet Index is at record low numbers in recent years including the wet year 2017 index.

The striped bass Summer Townet Index remains near record low in 2017.


Splittail Status end-of-June 2017

Last time I posted on splittail, it appeared that the species remained relatively abundant (though declining) in its core population centers in the Bay. I was concerned about population recruitment during the 2012-2015 drought and whether there were sufficient adults remaining to bring about a strong brood year in wet year 2017. The traditional summer and fall surveys will be the best indicator of success. At the end of spring, the best interim indicator is splittail salvage at south Delta SWP and CVP export facilities. In wet years, south Delta export salvage likely best reflects San Joaquin River splittail production.

I compare salvage in 2011 with 2017 in Figures 1 and 2 for the SWP and CVP, respectively. These were the only wet years since 2006. Wet years provide good spawning and rearing conditions for splittail. These conditions often create strong year classes of juvenile and adult splittail as shown in summer and fall fish surveys in the Delta and the Bay.

Though the density of juvenile splittail in salvage is lower in 2017 than 2011, winter and early spring flows were higher in 2017, which could have led to broader dispersal. Very high late winter and early spring flows in the lower Sacramento River system including the Yolo Bypass may have transported north-of-Delta splittail production directly to the Bay, bypassing the south Delta and its export facilities. Spring flows in the two years were similar in magnitude when young splittail traditionally move downstream through the Delta toward the Bay. It remains to be seen whether the difference in salvage plays out as a discrepancy in recruitment in the Bay populations. Local spawning recruitment in the Napa and Petaluma rivers and in Suisun Bay/Marsh could be strong in years like 2017 and could make up for lower recruitment from the Sacramento and San Joaquin river valleys. The primary concern is long term trends in the core adult population centers in the Bay that for now remain strong.

Splittail Salvage at SWP Byron Facility

Figure 1. Splittail salvage density (number per 10,000 cubic meters exported) at State Water Project Delta export facility in May and June 2011 and 2017.

Splittail Salvage at CVP Tracy Facility

Figure 2. Splittail salvage density (number per 10,000 cubic meters exported) at Central Valley Project Delta export facility in May and June 2011 and 2017.

Spring 2017 Delta Fish Salvage

Though it is counter-intuitive in a flood year, fish salvage has become a real problem this spring.

Total Delta exports reached 8,000 cfs in the first week in May, and salvage of salmon and splittail increased sharply (Figures 1 and 2). Normally, Delta standards limit export limits to1500 cfs in April-May in order to protect fish. However, higher exports are allowed when San Joaquin River inflows to the Delta are high. Even higher exports than the present 8,000 cfs are allowed, but the infrastructure cannot accommodate further exports in this wet year (demands are low and reservoirs south of the Delta are nearly full).

Figure 1. Salvage of Chinook salmon at south Delta pumping plants in spring 2017. Source: CDFW.

Figure 2. Salvage of splittail at south Delta pumping plants in spring 2017. Source: CDFW.

In past wet years, there were restrictions on south Delta exports in April and May to protect juvenile salmon, steelhead, splittail, and smelt that were rearing or passing through the Delta.  These restrictions also protected adult and juvenile sturgeon.  Figure 3 shows an example of Chinook salmon salvage in 1999.  The initial peak in February 1999 salvage was salvage of fry (1-2 inches).  The spring peaks were hatchery and river-reared smolts, primarily from San Joaquin River tributaries.  Both exports and salvage dropped after April 15.

In 2017, with the diversion of over half the San Joaquin River’s flow into the south Delta through the Head of Old River and other channels (Figure 4), there is a definite risk that high export levels will draw young salmon and splittail from the San Joaquin into the south Delta.  Once in the south Delta, they are subject to 8,000 cfs of diversions and a mix of tidal flows.  The risk is even higher than it might seem, because the reported State Water Project diversion is a daily average.  Water enters Clifton Court Forebay for only about one third of the hours in each day, during incoming tides.  The reported 5000 cfs is actually more like 15,000 cfs operating for those eight hours, adding to the pull toward the pumps of the incoming tides.

Reported salvage is just the tip of the iceberg, because predators eat up to 90% of juvenile salmon that enter the Forebay before these juveniles ever reach the salvage facilities.

In conclusion, the State Water Board needs to change the Delta standard.  It needs to limit spring exports even when San Joaquin flows are high.  In 2006 (Figure 5), the now-defunct Vernalis Adaptive Management Program limited April through mid-May exports despite high San Joaquin flows.  Salvage was markedly low during this period of limited exports.

If exports continue high through May and June in 2017, there will be detrimental effects on San Joaquin salmon, steelhead, and splittail, as well as on Delta smelt.

Figure 3. Salvage of Chinook salmon at south Delta pumping plants in winter-spring 1999. Note reduction in exports after mid-April. Source: CDFW.

Figure 4. High tide flows in the Delta at the beginning of May 2017. Blue represents positive downstream flows during high tides, where tides had minimal influence. Red denotes upstream tidal flow during incoming tides.

Figure 5. Salvage of Chinook salmon at south Delta pumping plants in winter-spring 2006. Note reduction in exports in early April. Winter-spring San Joaquin flows in 2006 were similar to those in 2017. Source: CDFW.