Category Archives: Water Quality

Partnership Shares Science to Find Fish and Water Solutions

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“This month six California and federal agencies representing water management, fish, and wildlife, along with the Sacramento River Settlement Contractors, signed onto the Sacramento River Science Partnership. The Partnership establishes an interagency science collaborative in which members will develop, share and discuss science to inform water management activities and protection of fish in the mainstem Sacramento River.” (8/25/20 News Release)

  •  The seven signatories will foster and advance science to inform sustainable solutions to water management challenges including conflicts between water supply delivery and fish survival.

The time when anyone thought that the problems confronting Central Valley salmon could be solved with more science is long gone. The problems and solutions have not really changed in the 40+ years I have been involved. And the problems are only getting worse. Why is it so hard to address them?

The Problems

As a consequence of rainfall, snowmelt, reservoir storage and release, and water diversions, flows in the Sacramento River, have become so low and erratic that they strand salmon spawning redds and create prolonged high water temperatures in the juvenile rearing and migration reaches of salmon. It is a wonder that there are any wild salmon left. Without hatcheries, there would be few if any salmon in the Central Valley at all.

Spring-Summer Water Temperatures

Spring-summer water temperatures in the lower Sacramento River are bad. They kill salmon and sturgeon, block migrations, lead to poor juvenile salmon growth, early migration, high predation, and cause huge predation problems for young hatchery and wild salmon. The high temperatures exceed state water quality standards and water project permit requirements. Yes, water temperatures were bad during the 2013-2015 critical drought, as might be expected (Figure 1). But they have also been bad in the five normal and wet years (2016-2020) since the drought (Figure 2). The safe level is 65°F, but the standard is set at 68°F, above which stress and higher mortality occurs. 68° is supposed to be an upper limit that should not be exceeded, and in past decades it rarely was. It is now the accepted norm, and even then it is not enforced.

In 2020 (Figure 3) spring water temperatures were detrimental to the upstream migration of endangered winter-run and spring-run salmon, emigrating juvenile fall-run salmon, and larval and juvenile sturgeon. High summer temperatures hinder migration of adult fall-run salmon and are detrimental to survival of winter-run fry, over-summering late-fall-run and fall-run salmon smolts, and rearing juvenile sturgeon.

Fall Drops in Water Levels

Often, usually in October-November, flow releases from Shasta reservoir drop sharply in response to decreasing downstream irrigation demands. The decreases lead to fall-run salmon redd dewatering in the upper river spawning area near Redding and poor habitat and emigration flows for winter-run and late-fall run juvenile salmon.

Stranding

Adult and juvenile salmon are stranded throughout the Sacramento River floodplain after winter-spring, high-flow events. In addition, drops in water surface elevation of four feet in the fall (Figures 4 and 5), soon after spawning de-water the vast majority of fall-run spawning redds in the 20-mile spawning reach downstream of Keswick Dam. Drops in flows after floodway weir spills (Figures 6 and 7) strand adult salmon and sturgeon that are migrating upstream, and also strand juvenile downstream emigrants in the Sutter and Yolo floodway bypasses.

Hatchery Releases

Releases of millions of hatchery-raised salmon and steelhead smolts in winter and spring into the lower Sacramento River from federal and state hatcheries compromise wild salmon and steelhead fry, fingerling, and smolt survival throughout the lower Sacramento River. Hatchery salmon and steelhead prey upon and compete with wild salmon and steelhead, and attract non-native predatory striped bass that also feed on wild salmon and steelhead.

Solutions

A new science plan for the upper reaches of the lower Sacramento River is not going to solve the problems that stem from failure to act on what science has told us for decades.

Solutions to the problems outlined above abound. These solutions are well documented in the Central Valley Salmon and Steelhead Recovery Plan (NMFS 2014) and other stakeholder plans.1 The most important solution, is water temperature limits in the lower Sacramento River, which were adopted decades ago in state water permits and water quality control plans. These limits designed to protect salmon are simply no longer enforced.

Figure 1. Water temperature in the lower Sacramento River from 2013-2015 critical drought years near Grimes, CA. Also shown is average for the past 11 years of record. https://nwis.waterdata.usgs.gov/nwis/

Figure 2. Water temperature in the lower Sacramento River from 2016-2020 post-drought years near Grimes, CA. Also shown is average for the past 11 years of record.

Figure 3. Water temperature in the lower Sacramento River in 2020 near Grimes, CA. Also shown is average for the past 11 years of record.

Figure 4. Sacramento River flows in fall of 2013 below Keswick Dam near Redding.

Figure 5. Sacramento River water surface elevation in fall of 2013 below Keswick Dam.

Figure 6. Spills of water from Sacramento River over Tisdale flood control weir during the period from December 2013 to February 2015. Source: CDEC

Figure 7. Spills of water from Sacramento River over Tisdale flood control weir during the period from January 2016 to May 2017. Source: CDEC

Franks Tract Futures Project

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The Franks Tract Futures Project is asking for additional comments on the State’s revised concept design.1 The project is an outgrowth of the State’s 2016 Delta Smelt Resilience Strategy, which recognized that Franks Tract is a death trap for state and federally listed Delta smelt.

The original design for the project included tide gates to keep salt and smelt from moving upstream from the western Delta into Franks Tract via the False River channel. Once in Franks Tract, the smelt would most assuredly not survive. A new design “transforms the project from an early focus on establishing habitat for the endangered Delta smelt to a project that has sought input from a broad range of stakeholders.” According to the project leader, Brett Milligan from University of California:

Balancing the project’s goals has been a challenge. The first round of this project, the feasibility study, met the water quality and ecology requirements but did not meet the recreational and local economy (requirements). We heard you loud and clear. More or less, this entire last year has been to try to bring in that third tier and to balance these and see if there’s a way that the project can meet all of these criteria and be beneficial to all. The original project design failed to earn public support after it was presented in January 2018. At a crossroads, the project managers made a critical decision. They scrapped the proposal and formed an advisory committee of stakeholders with varied interests in Franks Tract rather than try to force the initiative through the process, while fighting the public every step of the way.

The new design drops the barrier/gate option as “a non-starter,” Brett explained to me. But that was the essential element of the project – stopping salt (and smelt) intrusion into the interior Delta due to the pull of the south Delta export pumps. A temporary barrier has been installed in False River in drought years to protect Delta water supplies.

The conflict is over recreational access to Franks Tract from the west via False River. A similar barrier on Montezuma Slough further west in Suisun Marsh resolved a similar conflict with a boat passage lock that maintains boating access when the barrier is in use.

At this phase of design and permitting, it would seem wise to evaluate an alternative with the barrier that includes a similar boat passage facility, so that the affected public can understand the tradeoffs. That is the purpose of the environmental review process.

June 2020 Delta Outflow – New State Standard Needed

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I recommended a new June Delta outflow standard of 10,000 cfs in a post on June 23 2020. This increase from the current standard of 7000 cfs would keep salt and Delta smelt out of the Central Delta and better maintain adequate water temperatures for emigrating Central Valley salmon smolts.

In this post, I consider the recommended 10,000 cfs value in the context of how the California Department of Water Resources (DWR) and the Bureau of Reclamation (Reclamation) estimate Delta outflow as they manage Delta hydrology and federal and state exports from the south Delta. This should further explain why an increase in the June Delta outflow standard is necessary.

It helps to recall my description in a September 2019 post how DWR and Reclamation estimate Delta outflow: “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.“ This is different from the US Geological Service’s (USGS) method of calculating real-time outflow. As an example, I overlaid the DWR and USGS for the summer of 2018 (Figure 1).

The State’s D-1641 June water quality standard is: the monthly average of the average outflow for each day must meet or exceed 7000 cfs (monthly average of daily averages). DWR and Reclamation comply with this standard using their own estimation method, not real-time outflow. Figures 2 and 3 below show the differences in the DWR and USGS methods in May-June 2020.

In May-June 2020, DWR and Reclamation maintained Delta outflow (using their own estimation method) near 7000 cfs, except during a mid-May storm when estimated outflow reached a peak of 15,300 cfs (Figure 2). But viewed from a different perspective, there were significant dips in the USGS estimation of outflow during spring tides around June 5 and June 19. The DWR method of estimating didn’t pick up these dips at all. These periods where USGS showed negative net outflow showed up in the monitoring of salinity as well (Figures 4-6). Periods of low or negative outflow were also periods of high salinity at key Delta monitoring stations.

Although net daily Delta flows are relatively small compared to real-time tidal flows (Figures 7 and 8), net flows affect water quality and fish habitat conditions on a daily basis. The salinity data for May-June 2020 at False River (Figure 5) is particularly significant. (Note the spikes in salinity during spring tides around June 5 and June 19). False River is the gateway to Franks Tract. As salinity increases in False River, smelt will move upstream (towards lower salinity conditions) in Franks Tract. As I described in an April 28, 2020 post, Franks Tract is a “smelt trap” where smelt that enter almost invariably perish.

Increasing the standard for June Delta outflow so that the required monthly average of the average outflow for each day is 10,000 cfs, not 7,000 cfs, would not fully offset the effects of spring tides and the use of averaging in DWR’s method of calculating compliance. But it would help protect Delta habitat from salt intrusions during spring tides and keep the low salinity zone and young Delta smelt out of the Delta. Although DWR and Reclamation did a good job in May-June 2020 of staying above 7000 cfs each day using their calculated outflow method, adding an explicit minimum daily flow standard to the monthly flow standard could also help. This would likely have the result of reducing exports during periods of the spring tides in the monthly lunar tidal cycle.

Figure 1: Daily outflow estimated by DWR and USGS in summer 2018.

Figure 2. DWR’s calculated Delta outflow in May-June 2020. Note switch to July standard of 5000 cfs

Figure 2. DWR’s calculated Delta outflow in May-June 2020. Note switch to July standard of 5000 cfs outflow on July 1. Source: CDEC.

Figure 3. USGS’s estimate of tidally filtered Delta outflow as estimated in May-June 2020. Spring-tides occurred May 9, May 23 (not measured because of storm inflows), and also on June 5 and June 19. Note dips in outflow on June 5 and 19; these dips do not appear in DWR’s estimate in Figure 2.

Figure 4. Salinity (conductivity) in eastern Suisun Bay at Collinsville in May-June 2020. Note peaks in salinity during net negative outflow with spring tides on June 5 and 19 (see Figure 3).

Figure 5. Salinity (conductivity) in False River in west Delta in May-June 2020. Note peaks in salinity during net negative outflow with spring tides on June 5 and 19 (see Figure 3).

Figure 6. Salinity (conductivity) in eastern Suisun Bay at Pittsburg in May-June 2020. Note peaks in salinity during net negative outflow with spring tides on June 5 and 19 (see Figure 3).

Figure 7. Hourly river flow and tidally filtered flow in lower San Joaquin River channel in western Delta at Jersey Point in June 2020. Note highly negative peak flows with spring tides on June 5 and June 19.

Figure 8. Hourly river flow and tidally filtered flow in lower Sacramento River channel in western Delta at Rio Vista in June 2020. Note spring tides on June 5 and June 19.

A Case for Better River Flows and Delta Outflow in June

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When the State Water Board gets around to finally updating decades-old Central Valley water quality standards, it should bring back some old spring standards, keep some good ones, and add some new ones to provide essential protection to salmon, steelhead, sturgeon, smelt, and many other native fish populations.  One focus should be on improving survival of wild spring-run and fall-run salmon smolts migrating from Central Valley spawning rivers to the Delta, Bay, and ocean.

With its high spring water temperatures (Figure 1), 2020 is a good example of a solvable problem.  The survival of wild spring-run and fall-run salmon smolts depends on sufficient flows and low water temperatures in the spring.  This natural selection process, once tied to the natural spring snowmelt cycle,  has been disrupted by reservoir storage and water diversions.  Wild smolt emigration peaks in spring and extends into early summer (Figure 2).  Sturrock et al. (2019) found that late spring smolt survival suffered from poor emigration habitat conditions.  This affects population diversity because of the disproportionate loss of wild smolts in the late spring.

June Delta Exports

June exports in recent wet years (2011, 2017, and 2019) have averaged 9000-11,000 cfs under the State’s current State D-1641 standards.  This is a new impact (since 1995) that has manifested itself in a decreased proportion of wild fish in the salmon runs, thus threatening the very integrity of the populations and commercial and sport fisheries.  Under the previous D-1485 standards, south Delta project exports in June were limited to 6000 cfs in all year types.

June River Flows and Water Temperatures

June river flows should be sustained to help move smolts downstream and maintain water temperatures below stressful levels (less than 68°F/20°C).  River flows need to be adequate to keep water temperatures in the lower sections of the Sacramento River below 68°F/20°C, as recognized in the Central Valley Basin Plan’s water quality standard.  The flows needed to maintain water temperatures depend on air temperatures.  Over the past decade, water temperatures have exceeded the target in June in the lower Sacramento River even in wet years 2011, 2017, and 2019 (Figures 3 and 4).

June Delta Inflow

June Delta inflows need to be of sufficient magnitude to help salmon smolts pass through the Delta in a timely fashion, and not get diverted off-course toward the south Delta export pumps or succumb to huge numbers of predator fishes.  June flow entering the north Delta at Freeport needs to be maintained near 20,000 cfs to maintain water temperatures near 68°F/20°C (Figure 5).

June Delta Outflow

With 20,000+ cfs inflow and south Delta exports limited to 6,000 cfs, Delta outflow will be 10,000+ cfs (the other 4,000 cfs is from within-Delta diversions).  This is sufficient to keep the Low Salinity Zone west of the Delta and salmon smolts moving toward the Bay and Ocean.

Summary

In conclusion, the present year-round water temperature standard for the lower Sacramento River, 68°F/20°C, should be sustained through June.  New State Board standards should limit south Delta exports in June to 6,000 cfs to protect wild salmon smolts that are emigrating from Central Valley rivers.

Figure 1. Water temperature in the Sacramento River in the north Delta in spring 2020, along with recent 22-year median daily average. Water temperatures above 68°F/20°C severely stress emigrating salmon smolts. Water temperatures above 75°F/24°C are lethal to salmon. Water temperatures above 70°F/21°C hinder or block the migration of adult winter-run and spring-run salmon as they move upstream in spring.

Figure 2. “Timing of ocean entry of fish released from the Feather River hatchery (blue) and wild out-migrating (red) from 2002 to 2010. The area of each violin represents the proportion of fish out-migrating at that Julian day and is normalized to the total abundance of outmigrants for that year. The black lines represent the interquartile range (first to third quantiles). Hatchery release data for the Feather River Hatchery (FRH) are from Huber and Carlson (2015). Data for ’wild’ (unmarked) fall-run sized outmigrants are from the USFWS Chipps Island Midwater Trawl.” Source: https://www.nrcresearchpress.com/doi/10.1139/cjfas-2017-0273#.XuY87C0idvJ

Figure 3. Sacramento River flow and water temperature at the Verona gage just downstream of the mouth of the Feather River, 2008-2017. July 1 for each year is equidistant between the vertical lines.

Figure 4. Sacramento River flow and water temperature at the Wilkins Slough gage upstream of the mouth of the Feather River, 2008-2020. July 1 is one-quarter and three-quarters distance between each of the two-year period vertical lines.

Figure 5. Sacramento River flow and water temperature at the Freeport gage in the north Delta downstream of the mouth of the American River, 2016-2020. June flows (immediately to left of July 1 lines) of 20,000 cfs maintain water temperatures near 20°C.

 

American River Salmon Shortchanged

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The American River fall-run Chinook salmon are often referred to as a hatchery run. They are confined to the lower 20 miles of river below Folsom-Nimbus dams and are supplemented by Nimbus Hatchery smolt releases. Adult escapement (run size) is estimated from hatchery counts (Figure 1) and in-river spawning surveys (Figure 2). The run peaked with 100,000+ spawners from 2000-2004, after six wet years (1995-2000) and the initiation of large-scale releases of hatchery smolts to the Bay beginning in 1995 (Figure 3). After the initial success of Bay releases, the total numbers of smolts released dropped from the 8-12 million range to 4-5 million around the year 2000.

Since 2010, more releases have been shifted back to the river. The shift seems appropriate in wetter years like 2010, 2011, 2017, and 2019, but not in drier years like 2012, 2013, 2016, and 2018.1 Adult returns from dry year releases have been 2-to-7 times higher for Bay releases than for river releases. In 2020, a dry year, releases to the river occurred in early May, when downstream water temperatures were above the 68°F/20°C stress limit for juvenile salmon (Figure 4).

Unless winter-spring flows and water temperatures in the American River and Delta are improved,2 and problems with water temperatures during the fall spawning season are fixed,3 wild and hatchery production from the American River will continue to suffer. Until these issues are resolved, continued releases of American River hatchery smolts to the Bay remain necessary to sustain the salmon run.

For more on the American River hatchery program, see http://goldenstatesalmon.org/2020-salmon-update/ and https://www.facebook.com/NimbusHatchery/videos/932316603863844/ .

Figure 1. Fall-run salmon in-river escapement estimates for the American River (1952-2018).

Figure 2. Fall-run salmon hatchery escapement estimates for the American River (1955-2018).

Figure 3. Nimbus Hatchery releases to the American River (in-stream) and to the Bay 1991-2019.

Figure 4. Sacramento River water temperature (degrees C) in the northern Delta downstream from the mouth of the American River, from mid-April to mid-May 2020.