Category Archives: Water Quality

American River Fall-Run Status through 2018

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In my August 2017 post on the status of American River fall-run Chinook salmon, I analyzed recruitment through the fall 2016 spawning run. The 2016 run was a product of fall 2013 spawners (brood year 2013). In a May 2019 post, I discussed the survival of hatchery brood year releases through 2014. After record low escapement/recruitment in 2008 and 2009, there was a modest recovery from 2010-2014, followed by lower runs in 2015 and 2016 (brood years 2012 and 2013), the product of the 2012-2016 drought. Brood years 2012, 2013, and 2014 suffered from poor juvenile survival of hatchery and wild salmon in critical drought years 2013-2015. Overall production was sustained by Bay and coastal hatchery smolt releases (trucking and pen releases).

In this post, I update the status of the American River fall-run through 2018 with the addition of escapement estimates for the 2017 and 2018 runs. I also provide updated information on returns of hatchery brood year 2014 (2015 smolt releases). In addition, I provide a prognosis for the fall 2019 and future runs (returns/escapement).

2017 and 2018 Escapement

Poor river escapement in 2017 (Figure 1) likely reflects poor survival of naturally spawned salmon from fall through spring of critical drought water year 2015. The strong hatchery escapement in 2017 (Figure 2) reflects higher survival of brood-year 2014 hatchery releases to the Bay. Escapement improved in 2018 with higher river contributions from brood year 2015.

Updated Brood Year 2014 Hatchery Survival

Survival estimates based on hatchery coded-wire-tag returns for brood year 2014 (released in spring of critical drought year 2015) ranged from 0.3 to 1.4% (Figure 3). All were releases to Bay net pens. The two higher (good) survival rates were from mid-May releases, when outflows were slightly higher and Bay temperatures were cooler (Figure 4). Differences in survival among and within years reflect a positive relationship between survival and Delta outflow on the date of release (Figure 5).

Brood Year 2015 Hatchery Survival

Survival of hatchery brood year 2015 (2018 hatchery counts, Figure 2) was slightly depressed, possibly as a consequence of more of the hatchery smolt production being released into the lower American River rather than trucked to Bay pens (Figure 6). Early tag returns from the 2016 releases indicate much higher survival of the Bay pen releases than river releases (Figure 6).

Prognosis for Brood Year 2016 (Fall 2019 Run)

River flows and Delta outflow conditions were much better in springs of 2016-2019, wetter water years, than in the springs of the 2013-2015 critical drought years (Figure 7). Survival of naturally produced fish and hatchery fish released into the river should show improvements given the wetter conditions. Survival of hatchery fish released to the Bay should be good given higher Delta outflows. It may take wet-year-type spring river flows (Figure 8) or timed pulsed flows to achieve high survival of river smolt releases. River-release survival rates from 2016 and 2018 release groups are likely to be depressed since these water years were saw only moderate flows after mid-April, whereas river-release survival rates from the abundant water years 2017 and 2019 are likely to be good, as in 2010 and 2011.

Figure 1. River spawner estimates 1952-2018.

Figure 1. River spawner estimates 1952-2018.

Figure 2. Hatchery spawner estimates 1955-2018.

Figure 2. Hatchery spawner estimates 1955-2018.

Figure 3. American River Hatchery smolt release group survival (%return) for 2009 to 2015. Data Source: https://www.rmis.org/.

Figure 3. American River Hatchery smolt release group survival (%return) for 2009 to 2015. Data Source: https://www.rmis.org/.

Figure 4. Water temperature and salinity (EC) near American River Hatchery smolt net-pen release sites in spring 2015. Red dots are dates when smolts were released.

Figure 4. Water temperature and salinity (EC) near American River Hatchery smolt net-pen release sites in spring 2015. Red dots are dates when smolts were released.

Figure 5. Smolt Bay-pen release group survival rate versus Delta outflow at the time of release.

Figure 5. Smolt Bay-pen release group survival rate versus Delta outflow at the time of release.

Figure 6. Brood year 2015 hatchery smolt releases in spring 2016.

Figure 6. Brood year 2015 hatchery smolt releases in spring 2016.

Figure 7. Delta outflow spring 2015-2019.

Figure 7. Delta outflow spring 2015-2019.

Figure 8. American River flow at Fair Oaks in spring of selected years in last decade.

Figure 8. American River flow at Fair Oaks in spring of selected years in last decade.

 

 

Analyzing Fish Population Dynamics in the Bay-Delta

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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.

Pre-1970

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.

Post-1970

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.

Post-1990

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.

Conclusion

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 ↩

Twists and Turns of 2019 Fall X2

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The California Department of Fish and Wildlife (CDFW), in a September 24, 2019 letter from Director Charlton Bonham, asked the US Bureau of Reclamation (Reclamation) to immediately implement “Fall X2” flows. Fall X2 increases Delta outflow from August 15 through October of wetter water years to protect Delta smelt. Fall X2 is a condition in the federal 2008 Smelt Biological Opinion for the Long-term Operation of the Central Valley Project (CVP) and the State Water Project (SWP).

Reclamation had issued a perfunctory Environmental Assessment in August 2019 to purportedly analyze the effects of eliminating Fall X2 in 2019. Reclamation claimed authority to unilaterally rescind the condition because the Biological Opinion has provisions for “adaptive management” of the condition.1 In response to Bonham’s letter, Reclamation, on October 1, backed away from rescinding Fall X2.

Over the past week, X2, the focused location of the 2 parts per thousand (ppt) salinity level in the Bay-Delta, had moved upstream several kilometers from its prescribed km 74 location.2 Salinity increased (Figure 1) because Delta outflow declined (Figure 2). X2 had moved nearly half way to the km 81 location to which Reclamation had proposed to operate in 2019. The lower Delta outflow appeared in part to be in response to reduced releases from Reclamation’s Folsom Reservoir to the lower American River on September 25-26 (Figure 3), which in turn showed up as reduced Delta inflow at Freeport on the Sacramento River below the mouth of the American River (Figure 4). The state increased Oroville Reservoir releases by 2,000 cfs over the past week to make up for falling Shasta releases into the lower Sacramento River.

In response to its decision to implement Fall X2 after all, Reclamation increased flow releases from Folsom Reservoir into the lower American River on September 30, thus keeping Delta inflows as measured at Freeport above 18,500 cfs. The state decreased south Delta exports by 3000 cfs (50%) on 28 and 29 September. X2 is again at km 74.

Figure 1. Salinity (EC) at Mallrd Slough near Chipps Island in Suisun Bay (about km 74) 2-30 September, 2019. X2 (about 3800 EC) was again at this location by Sep 30.

Figure 1. Salinity (EC) at Mallrd Slough near Chipps Island in Suisun Bay (about km 74) 2-30 September, 2019. X2 (about 3800 EC) was again at this location by Sep 30.

Figure 2. Measured daily average Delta outflow near Pittsburg in Suisun Bay 17-25 September 2019. After low outflows on 25-26 September the subsequent rise through 30 September was in large part due to cessation of monthly spring tides in addition to increased Oroville and Folsom reservoir releases.

Figure 2. Measured daily average Delta outflow near Pittsburg in Suisun Bay 17-25 September 2019. After low outflows on 25-26 September the subsequent rise through 30 September was in large part due to cessation of monthly spring tides in addition to increased Oroville and Folsom reservoir releases.

Figure 3. Daily flows in the lower American River - Aug1 to Sep 30, 2019.

Figure 3. Daily flows in the lower American River – Aug1 to Sep 30, 2019.

Figure 4. Daily average Sacramento River flow at Freeport in north Delta during September 2019.

Figure 4. Daily average Sacramento River flow at Freeport in north Delta during September 2019.

  1. See “Reclamation’s Proposed Delta Smelt Fall Habitat Action In 2019” at http://calsport.org/fisheriesblog/?p=2813.  Reclamation is also trying to permanently eliminate Fall X2 in a new Biological Opinion.  See description in http://calsport.org/news/a-fresh-disaster-for-fish-bureau-of-reclamations-new-plan-for-long-term-operations-of-the-cvp-and-swp-water-export-business/ ↩
  2. 74 kilometers from the Golden Gate. ↩

Reclamation’s Proposed Delta Smelt Fall Habitat Action In 2019

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The US Bureau of Reclamation (Reclamation) is proposing a “Delta Smelt Fall Habitat Action” that would eliminate the requirement to increase outflow from the Delta in the late summer of this wet water year.1 The “Fall X2” flow increase that Reclamation has placed on the chopping block is a major provision in the 2008 Delta smelt biological opinion (BiOp). Reclamation describes the substitute proposed Action in a summary its webpage:

The Proposed Fall Habitat Action (Proposed Action) for Delta Smelt habitat in Water Year (WY) 2019 will achieve the Action 4 objective. Action 4 of the 2008 BO requires adaptive management to ensure that the implementation addresses the uncertainties about the efficiency of the action. Action 4 also states that as new information is developed and as circumstances warrant, changes by the Service to the Fall X2 action itself may be necessary. The Proposed Action is a plan to adaptively manage and modify its operation of the CVP/SWP under RPA Action 4.2

In brief, the “circumstances” that “warrant” this “adaptive management” are that getting rid of Fall X2 will allow Reclamation to export more water from the Delta this fall.

In August 2019, Reclamation issued an Environmental Assessment (EA) of the Proposed Fall Habitat Action. Though the Action will unravel a major component of the 2008 Biological Opinion for smelt, the comment period was 15 days. CSPA submitted comments; some of them are restated below, in response to citations from the “Effects Analysis,”3 an appendix to the Environmental Assessment.

The Effects Analysis quotes the BiOp to portray the Proposed Action as a scientific investigation, stating:

“[T]here is a high degree of uncertainty about the quantitative relationship between the size of the Action described above and the expected increment in Delta Smelt recruitment or production.” (p. 1).

Comment: After 2011, it has been nearly impossible to measure population response to changes in management because the smelt population has become so low. Likewise, a negative response cannot be detected at the present population level. The only certainty to be gained from harming a nearly extinct population even more is that Reclamation will increase exports from the south Delta.

The Effects Analysis selectively calls out results of the first implementation of the Fall X2 requirement in 2011:

“Abiotic habitat did increase in 2011 as predicted from the AMP, but other variables such as zooplankton abundance were too variable to draw a conclusion, and Delta Smelt growth rate comparisons remain incomplete as of 2019.”  (p.2)

Comment:  Following implementation of Fall X2 flows, smelt abundance increased sharply in the fall 2011 index. A quick look at zooplankton 2011 vs 2010 (Figure 1) also indicates an increase in zooplankton (key smelt food source) in Suisun Bay/Marsh in 2011.

Figure 1. Zooplankton (key Delta smelt food source) in September 2011 and 2010.
Note increased abundance downstream in 2011.

The Effects Analysis tries to explain the lack of response of Delta smelt to the 2017 Fall X2 action as a function of water temperature, concluding that the action was just futile:

In 2017, a Fall X2 adaptive management action was implemented. The results of the 2017 monitoring program were evaluated in the IEP’s 2019 draft FLOAT-MAST, which concluded that summer water temperatures were a major factor in the condition of Delta Smelt in 2017, stating at p.102: Given the long periods in July and August >22C we are confident that water temperature had a major negative effect on Delta Smelt in 2017 and is likely a primary factor in the lack of response of the Delta Smelt population to the high flows.  And at p. 104: Dynamic biotic components were somewhat better in 2017; however, the lack of response of the Delta Smelt population suggests that any benefits of changes in the habitat were minimal. (p. 3)

Comment:  It is true that recruitment of Delta smelt in 2017 was exceptionally low, despite the Fall X2 action.  This is because the number of adult spawners in 2017 was at a record low (Figure 2).

Fall 2017 water temperatures were slightly higher in the west Delta at Jersey Point compared to 2011 (Figure 3).  However, fall 2017 water temperatures were not unusually high compared to fall 2011 for Freeport or for Rio Vista in the Sacramento River channel of the Delta (Figure 4).  June and July Sacramento River water temperatures were substantially higher in 2017 than in 2011, because June and July Sacramento River flows were much lower in 2017 compared to 2011 (Figure 5). 

In general, spring habitat conditions were poorer in 2017 than in 2011:  2017 had lower spring Delta outflows (Figure 6) and much higher south Delta exports (Figure 7).

In sum, the 2017 fall index for Delta smelt was unusually poor because of poor conditions for Delta smelt in the spring and summer.  However, the response of longfin smelt to the implementation of Fall X2 in 2017 had a better outcome (Figure 8).  Despite poor number of spawners, the 2017 recruitment of longfin smelt per spawner was high. 

These data undermine Reclamation’s conclusion that the 2017 Fall X2 action had no benefit. 

Figure 2. Log vs Log plot of fall FMWT Index of Delta smelt (recruits) vs previous fall index (spawners). Blue years are wet years. Red years are dry and critical water years. Year types are determined by the California Department of Water Resources for the Sacramento River runoff to the Bay-Delta Estuary (http://cdec.water.ca.gov/cgi-progs/iodir/WSIHIST).

Figure 3. Comparison of Jersey Pt habitat conditions in 2017 versus 2011. Tidally filtered flow data were not available for 2011.

Figure 3. Comparison of Jersey Pt habitat conditions in 2017 versus 2011. Tidally filtered flow data were not available for 2011.

Figure 4. Freeport and Rio Vista water temperatures 2013-2019.

Figure 5. Freeport flow and water temperature summer 2011 and 2017.

Figure 6. Summer Delta outflows in 2011 and 2017.

Figure 7. South Delta federal exports (TRP) and state exports (HRO) in 2011 and 2017.

Figure 8. Longfin smelt spawner-recruit relationship, with improved recruitment in 2011 and 2017. Wet year blue, dry year red. Source: http://calsport.org/fisheriesblog/?p=2513

So, after stating inaccurate and misleading reasons why the Fall X2 action is not effective, the Effects Analysis offers inaccurate and misleading reasons why not implementing Fall X2 and instead fussing with the Suisun Marsh Salinity Control Gates (SMSCG) will be a positive switch.

“Forecast of salinity conditions in the Delta indicate that operating to an X2 of 80 km along with SMSCG operations in September and October would result in suitable salinity conditions (< 11,000 uS/cm) in the western Delta including Suisun Marsh, Grizzly Bay, and Honker Bay during these two months.”  (p. 17)

Comment:  Operating the SMSCG tide gates, while not implementing Fall X2, will push more Delta outflow into Suisun Marsh, with less outflow reaching eastern Suisun Bay.  Both actions would potentially negatively affect Delta smelt compared to implementing the Fall X2 Action per the existing BiOp.

“However, as explained above, this estimate of abiotic habitat index does not account for the habitat created in Suisun Marsh through the operation of the SMSGC, which would increase the index.” (p. 31)

Comment:  moving outflow through SMSGC reduces habitat in eastern Suisun Bay, and subsequently traps any Delta smelt in Suisun Marsh once the gates are again closed.

Conclusion:  Stock-recruitment models show a strong positive population response for Delta smelt in 2011 (see Figure 2) and longfin smelt in 2017 (see Figure 8).  The strong population responses in 2011 and 2017 offer a strong case for implementing the Fall X2 action in 2019.  Reclamation’s only justification for eliminating the Fall X2 action in 2019 is to increase water available for export.  Biology has nothing to do with it.

Delta Outflow Measurement

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Delta outflow has been estimated by state and federal agencies for over 50 years.  The Department of Water Resource’s Delta Total Outflow is a daily-average algorithm calculated in cubic feet per second (cfs) for Station DTO, a hypothetical location near Chipps Island in Suisun Bay.  The federal Bureau of Reclamation’s Delta Outflow estimate is calculated similarly and presented as a daily average flow in cubic feet per second on Reclamation’s website.

Now a third estimate of Delta Outflow is available from the federal US Geological Survey on one of its websites (https://waterdata.usgs.gov/nwis/inventory?agency_code=USGS&site_no=380245121532301).  This site has daily average estimates for a “gage” near Chipps Island since summer of 2016.  The estimate is from tidally filtered flow/stage data.

A comparison of the DWR and USGS estimates is shown below in Figures 1 and 2.  The two estimates are very similar.  A closer comparison during the low-flow summer periods of 2018 (Figure 3) and 2019 (Figure 4) indicates significant differences, or at a minimum a modicum of uncertainty in one or both of the estimates.  The average flow in the DWR data for 2018 data is about 10% higher over the period than the USGS data.  The role of tides or tidal filtering in the USGS estimate is a likely factor in the difference.  Under high seasonal tide periods (termed spring tides), outflows can fall to near zero, with major ramifications to salinity and water over the entire Bay-Delta, especially in the high export summer season.

The state’s current water quality control plan for the Delta includes objectives for Delta outflow (Figure 5).  The objectives are stated as a monthly average.  The low level of the objectives 3000-8000 cfs should give one pause as to the level of protection that these objectives provide to public trust resources like fish.  The Water Resources Control Board is in the process of updating its plan and water quality objectives.

In past posts, I have advocated for daily salinity standards for the Delta rather than bi-weekly or monthly objectives for outflow, flow, export, and salinity.  Such daily standards could be readily planned for, managed, monitored, and assessed for effectiveness.

Figure 1. USGS estimate daily Delta outflow Sep 2016 to Sep 2019.

Figure 2. DWR estimated daily Delta outflow Sep 2016 to Sep 2019.

Figure 3. Estimated daily outflow by DWR and USGS summer 2018.

Figure 4. Estimated daily outflow by DWR and USGS summer 2019.

Figure 5. Delta outflow objectives in state’s water quality control plan.