Sacramento River Low Flows and High Water Temperatures Violate State Standards for lower Sac River and Delta - Lethal for Salmon and Smelt

Low flows in the lower Sacramento River above the Feather River and warm flows from the Feather River are compromising the summer habitat of smelt and salmon in the lower Sacramento River and the Delta, violating state and federal water quality standards.

Lower Sacramento River at Wilkins Slough

The Sacramento River at Wilkins Slough at river mile 118, 63 miles upstream of the Sacramento Delta, has low flows and high water temperatures (Figure 1).  The high water temperatures are a violation of the 68oF (average daily) water quality standard and are stressful to migrating salmon.

Lower Sacramento River at Verona below mouth of Feather River

The lower Sacramento River 50 miles downstream of Wilkins Slough at Verona, just downstream of the mouth of the Feather River, has near lethal water temperatures, far above the water quality standard (Figure 2).  The high temperatures are likely due in part to recent increased releases from Oroville Reservoir to lower water levels for the spillway repair project.

Lower Sacramento River in Delta

The lower Sacramento River at Freeport in the north Delta, 25 miles downstream of Verona, has near lethal water temperatures for Delta smelt (Figure 3).   The high temperatures are likely due in part to recent increased releases from Oroville Reservoir to lower water levels for the spillway repair project.  The north Delta water temperatures are also high in part due to lower than normal net river flow (as measured at Rio Vista 20 miles downstream of Freeport – Figure 4).  The low flows have also led to encroaching salinity at Emmaton several miles downstream of Rio Vista (Figure 5), also in violation of water quality standards.

Figure 1. Sacramento River at Wilkins Slough flow and water temperature in May-June 2018. The water temperature standard for the lower Sacramento River is 20°C (68°F).

Figure 2. Sacramento River at Verona water temperature 6/15-6/26, 2018. The water temperature standard for the lower Sacramento River is 20°C (68°F).

Figure 3. Sacramento River at Freeport water temperature 6/15-6/26, 2018. The water temperatures above 72°F are stressful to Delta smelt.

Figure 4. Rio Vista daily average historical and 2018 flow May-June.

Figure 5. Salinity (EC) at Emmaton near Rio Vista. The standard of 450 EC (uS/cm) was exceeded from 6/15 to 6/18, 2018. The standard is necessary to keep the low salinity zone, critical habitat for Delta smelt. west of the Delta.

Coho Salmon Fishery Options in California

The two sub-adult hatchery coho pictured above were recently caught in Puget Sound near Seattle, in a mark-selective fishery (note adipose fins missing on all hatchery coho as in California) where all wild fish (intact adipose fin) must be released. This Washington state sport fishery is hugely popular.1 These hatchery fish reside in the Puget Sound year-round, unlike their wild counterparts.

Coho are native to the California coast and are listed under the state and federal endangered species acts, as they are in Oregon and Washington states. Coastal coho are supplemented by four hatcheries in California. No coho may be kept in California fisheries. Coho were once planted in California reservoirs and supported popular fisheries.

Coho recovery efforts over the past several decades have had mixed results. Information on coho in California can be found at: https://www.wildlife.ca.gov/Conservation/Fishes/Coho-Salmon . The goal of the 2004 Coho Recovery Strategy to allow fishing has not been met:

Recovery Strategy GOAL VI: Reach and maintain coho salmon population levels to allow for the resumption of Tribal, recreational, and commercial fisheries for coho salmon in California.

So why not establish mark-selective fisheries for coho in coastal bays in California (e.g., Monterey, San Francisco, Tomales, and Humboldt bays)? The same issues and conflicts in California occur in the Puget Sound fishery. Why not help the underfunded California Coho Recovery Program with revenue generated from such a hatchery coho fishery?

For more information on coho recovery, see: http://www.westcoast.fisheries.noaa.gov/.

Enhancing Pelagic Habitat Productivity in the North Delta Is it too late to save the Delta smelt?

The Bureau of Reclamation recently released an Environmental Assessment for the Sacramento Deep Water Ship Channel Nutrient Enrichment Project. The proposed project would directly release nitrogen nutrients into the Ship Channel, which runs from West Sacramento to Cache Slough, north of Rio Vista.  The project is designed to stimulate plankton blooms in the North Delta as part of the Delta Smelt Resilience Strategy, which describes the goal as follows:

The purpose is to determine if the addition of nitrogen can stimulate plankton (fish food organisms) production in a section of the ship channel, which is isolated from the Delta in terms of water flow.

Adding nitrogen to the ship channel will indeed stimulate plankton productivity.  Only a few miles away, regional governments have spent decades in removing nitrogen (most recently, ammonia) from the effluent of the Sacramento Regional Wastewater Treatment Plant to reduce production of blue-green algae in the Delta.  The City of West Sacramento already seasonally releases high nutrients, metals, and salts into the Ship Channel.  Adding more nitrogen could easily increase toxic blue-green algae problems in the Delta, similar to the bloom that recently led to the recreational closure of southern California’s Diamond Valley Reservoir, which receives Delta water.

There is higher plankton productivity in the Ship Channel than in nearby Delta channels because the Ship Channel has longer residence time, higher nutrients,  and higher water temperatures.  The broken gate on the Ship Channel’s northern entrance contributes to these conditions.  However, lack of circulation also leads to nitrogen depletion and declining plankton production, and there is limited seasonal replenishment of nitrogen.

The Delta Smelt Resilience Strategy is considering increasing flows into the north Delta from the Colusa Basin Drain, Fremont Weir, and the Ship Channel to stimulate Delta plankton blooms.  The biggest problem with these sources is high spring-through-fall water temperatures (Figures 1-3).  Water temperature is certainly the greatest limiting factor in the north Delta for Delta smelt; adding nitrogen will not fix this problem.

Fixing the gate at the north end and allowing cooler Sacramento River water (strong American River influence) into the channel (Figure 4) would reduce water temperatures in the Ship Channel.  Just a few degrees can be life or death for Delta smelt.  Increased entry into the Ship Channel of Sacramento River water would also introduce more nitrogen, potentially reducing the need to fertilize the Ship Channel with crop dusters.

Figure 1. Water temperature in the Yolo Bypass downstream of the entrance of the Colusa Basin Drain.

Figure 2. Water temperature in the Sacramento River Deep Water Ship Channel.

Figure 3. Water temperature in the lower Yolo Bypass toe drain canal near Liberty Island.

Figure 4. Water temperature in the Sacramento River near Freeport downstream of the entrance to the Sacramento River Deep Water Shipp Channel.

Gross Violation of Water Quality Standards for Water Temperature in Lower Sacramento River Further Degradation of Salmon Habitat

Water temperatures in the lower Sacramento River over the past month have often exceeded water quality standards that protect salmon and other beneficial uses (Figures 1 and 2).  Water temperatures at or above the standard of 68oF adversely affect adult and juvenile salmon.  Water temperatures can meet the standard if the Bureau of Reclamation maintains flow in the Sacramento at Wilkins Slough at 6000-8000 cfs, depending on air temperature.  The Bureau of Reclamation has maintained such flows in the past to meet water quality standards and terms in its water rights permits (Figure 3).  Shasta Reservoir water storage is 102% of normal as of June 18, 2018.  Water diversions from the Sacramento River upstream of Wilkins Slough are approximately 6,000 cfs, with 100% allocation to CVP contractors under water right permits.  For more on the effects on salmon, see past posts.

Figure 1. Sacramento River flow and water temperature at Wilkins Slough in lower Sacramento River: mid-May to mid-June 2018. Red line denotes water quality standard. Source: CDEC.

Figure 2. Sacramento River water temperature at Verona in lower Sacramento River: mid-May to mid-June 2018. Red line denotes water quality standard. Source: CDEC.

Figure 3. Historical and recent flow at Wilkins Slough. Source: USGS.

2016-2017 Salmon Crash
Sacramento River Fall-Run Salmon Decline

In an April 2018 post, I revisited the 2007-2009 salmon crash and warned of the current 2016-2017 crash.  In an April 2017 post, I opined on the status of population and its future given the population crashes.  In this post, I update the population data with preliminary estimates of the 2016 and 2017 runs, including (1) the in-river estimate from the spawning grounds between Keswick Dam and Red Bluff (Figure 1), and (2) Coleman National Fish Hatchery (CNFH) and Battle Creek (Figure 2).

I developed a stock-recruitment relationship using the in-river data shown in Figure 1.  A plot of the population-produced from spawners three years earlier (Figure 3) shows extremely poor runs for 2016 and 2017, given the number of parental spawners three years earlier.  The red numbers reflect drought conditions winter-spring of 2014 and 2015, when these broods were rearing and migrating in the Sacramento River in the first few months of their lives.  The earlier posts covered the factors that led to poor survival in the drought years.

Forecasts for the 2018 run are mixed.  Higher jack numbers in the 2017 run likely foreshadow improvements in the adult 2018 run.  Based on the Figure 3 relationships, the higher 2015 run, along with normal year conditions (a green number) for winter-spring 2016 compared to 2014 and 2015, would also indicate an improved run for 2018.   A forecast for 2019 and 2020 runs, given the poor runs in 2016 and 2017, is risky at best, despite reasonably good winter-spring conditions in 2017 and 2018 compared to drought years 2014 and 2015.  A lack of recovery to 2015 spawner levels in the fall 2018 run would be a serious concern.

Figure 1. Run size estimates (escapement) of fall-run Chinook salmon from spawning grounds in the upper Sacramento River between Keswick Dam and Red Bluff from 1975 to 2017.

Figure 2. Run size estimates (escapement) of fall-run Chinook salmon from the Coleman National Fish Hatchery on Battle Creek near Red Bluff from 1975 to 2017.

Figure 3. Spawner-recruit relationship for fall-run in-river estimates of run size from Figures 1 and 2. Number indicates spawner estimate for that year (y-axis) as derived from spawners three years earlier (x-axis). Color indicates winter-spring rearing-migration conditions for that brood (winter-spring 2015 for spawners in 2017). Red denotes dry year in first winter-spring. Green is for normal years. Blue is wet years.