Category Archives: Water Quality

Follow-up on Spring 2020 Sacramento River Conditions

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In a recent post (May 6, 2020), I discussed the need to increase flows in the lower Sacramento River to reduce water temperatures for emigrating juvenile spring-run and fall-run hatchery and wild Chinook salmon. I recommended maintaining water temperatures below 65°F/18°C per the scientific literature. Water managers increased flows (or reduced diversions) on about May 11 (Figure 1), and with the help of cooler weather (Figure 2), water temperatures came down significantly through the lower Sacramento River (Figures 1, 3, and 4).

The National Marine Fisheries Service (NMFS), California Department of Fish and Wildlife (CDFW), and US Bureau of Reclamation (BOR) have begun a multi-year study to evaluate the potential survival benefits for juvenile spring-run and fall-run Chinook salmon of managed spring flow pulses in the Sacramento River.1 Such action is prescribed in the NMFS 2019 biological opinion for the federal Central Valley Project. The problem with the prescription is that it applies only in wetter years when there is high Shasta Reservoir storage (4 million acre-ft end-of-April), while the need is greatest in drier years when reservoirs capture most if not all the water from limited precipitation events.

But why study the concept with 50 years or more of data available? Just looking at this spring’s data shows the role flow can play in keeping temperature below levels that are known to increase salmon mortality. In this blog I have shown over and over the order-of-magnitude benefits to population recruitment that comes from maintaining flows and water temperature. The scientific literature is replete with analyses of the effects of water temperature on salmon. We know that temperatures in the lower Sacramento River on May 9-10 were bad for immigrating adult salmon and emigrating juvenile salmon, so why not acknowledge the problem and correct it?

And why just study the benefit of a single flow pulse? Results would depend on so many factors. In Figure 1, weather forecasts indicated the May 7-9 heat wave days ahead, so why wasn’t the flow pulse applied earlier? Or were water managers simply responding to water demands or violations in water quality standards that occurred May 8-10 at Verona?

In any case, the May 2020 example shows that flows and water temperatures in the lower Sacramento River need to be actively managed to protect salmon.

Figure 1. Water temperature and streamflow in the Sacramento River at Wilkins Slough and Verona May 1-15, 2020. See Figure 4 for gage location.

Figure 2. Air temperature at Hood near Freeport May 1-15, 2020.

Figure 3. Freeport gage water temperature and daily average flow (tidally filtered) May 1-15, 2020. Figure 4 for gage location.

Figure 4. Gage stations in lower Sacramento River

 

  1. A link to the draft study plan: https://1drv.ms/b/s!ArkjAKW4WdKRwCWsW3cnyJdS5Zac ↩

Klamath’s Scott River Salmon and Steelhead in Trouble

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Scott River – April 2020

The Scott River is a major contributor to Klamath River salmon and steelhead runs.1 The fry of fall-run Chinook and Coho salmon that spawned in the Scott system this past fall-winter are now leaving their gravel beds. Steelhead are completing their spawning run. These salmon and steelhead are in for a tough year because flows are low (Figure 1), precipitation has been minimal (Figure 2), and the snowpack is well below average (Figure 3).

The state of California needs to step up to protect these iconic and socio-economically important wild salmon and steelhead runs and the critical habitats that support them. The State Water Resources Control Board, supported by the California Department of Fish and Wildlife, needs to maintain adequate flows in the Scott River through the fall. If the state does nothing, the river will dry up by summer, and most of the young fish will die.

The State Water Board and CDFW must control and carefully monitor surface diversions and groundwater extractions for pasture and hay irrigation. Otherwise, the river and all its aquatic life will die, and domestic-use water will dry up.

Coho salmon are a state and federally listed endangered species protected by law. Water rights issued and managed by the State Water Board require protection of these natural resources. Fish habitat is protected by state laws; state agencies need to enforce these laws. Local entities such as water districts, resource conservation districts, water and land trusts, tribes, communities, and landowners need to pitch in.

Figure 1. Streamflow in the Scott River September 2019 to April 2020, plotted next to 70-year average (log scale).

Figure 2. Monthly average precipitation in inches at Callahan, CA over past two decades. Note near zero precipitation in Feb 2020. Source: CDEC.

Figure 3. Snow survey data summary for Scott River and Shasta River watersheds in 2020. Source: CDEC.

Adult Winter-Run Salmon Migration in Jeopardy under New Biological Opinion

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As we enter May 2020, winter-run Chinook salmon are in the middle period of their near 300-mile adult migration up the Sacramento River to spawning grounds below Shasta Dam near Redding, CA. These adult salmon are in jeopardy this spring from low flows and high water temperatures in the lower Sacramento River. The new federal biological opinion on the long term operation (BO-LTO) of federal Central Valley Project (CVP) and State Water Project (SWP) that went into effect in October 2019 is not protecting these migrating adult winter-run.

State of California water right permits for the CVP/SWP and the Central Valley Basin Plan have prescribed standards (e.g., maximum allowed lower Sacramento River temperature of 68°F). However, federal and state agencies have largely ignored these standards.1

Figures 1-4 depict the basic problem: water temperatures in the lower 120 miles of the Sacramento River from Wilkins Slough downstream to Rio Vista are in excess of stressful or near-lethal levels, levels known to hinder or even block migrations, and levels known to reduce (1) survival, (2) successful spawning, and (3) subsequent egg viability of the adult salmon.

At a minimum, water temperature objectives in the Basin Plan and Water Right Order 90-05 should be met. It is simply unacceptable for water temperatures at Verona (RM 80) to be 70°F or higher. Maintaining lower river flows near 6000 cfs near Wilkins Slough (RM 120) and near 10,000 cfs near Verona (below the mouth of the Feather River) is necessary to meet temperature objectives. Such levels would also reduce water temperatures downstream in the Delta (Freeport and Rio Vista). The 68°F objective in the Basin Plan is a year-round standard and requirement of the water right permit for the state and federal water projects in the Sacramento River Basin.

The 68°F objective was met more frequently in recent below normal water years 2012, 2016, and 2018, at least well into the month of May (Figure 5). It was also met more frequently later into the spring in the 2008-2010 drought period (Figure 6).

In conclusion, there is a continuing eroding of the Sacramento River temperature standard, which appears to have accelerated under the new BO-LTO. Higher spring water temperatures are a serious risk to the winter-run salmon population.

Figure 1. April 2020 Sacramento River water temperatures near Red Bluff (RDB, RM 240), Wilkins Slough (WLK, RM 120), and Verona (VON, RM 80). Blue line is upper limit of optimal migration temperature. Green line is safe limit. Orange line is beginning of stressful level. Red line is beginning of lethal or avoidance/blockage level.

Figure 2. April 2020 Sacramento River water temperature and flow near Wilkins Slough (WLK, RM 120). 20°C is equivalent to 68°F.

Figure 3. April 2020 Sacramento River water temperatures and tidally filtered flow near Freeport in the Delta.

Figure 4. April 2020 Sacramento River water temperatures and tidally filtered flow near Rio Vista in the Delta.

Figure 5. Spring water temperatures in the lower Sacramento River at Wilkins Slough (WLK) and Verona (VON) in 2012, 2016, and 2018 below-normal water years. Red line is Basin Plan maximum objective.

Figure 6. Spring water temperatures in the lower Sacramento River at Verona (VON) in 2008, 2009, and 2010. Red line is Basin Plan maximum objective.

 

  1. The BO includes this statement on page 230: “The Spring pulses are also expected to benefit adult winter-run Chinook salmon migrating up the Sacramento River later in the spring. The spring pulses would provide improved water flows that in turn provide cooler temperatures (improved Water Temperature), and allow for better passage conditions”. However, the BO-LTO prescribes no spring flow pulses at all for drier years like 2020. ↩

Franks Tract – Smelt Trap

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In a May 2019 post, I described the central Delta as a salmon trap for juvenile salmon. This post describes the “smelt trap.”  Franks Tract in the central Delta (Figure 1) is a longfin and Delta smelt trap.  Longfin smelt were vulnerable to the trap in March 2020 (Figures 2 and 3).  Flow was reversed in False River (Figure 4) because of south Delta exports.

It’s not just the net flow that makes Franks Tract a smelt trap.   It is also tidal pumping of 50,000 cfs in-and-out.  What goes into Franks Tract on the flood tide does not come back out the same (Figures 5-9).  It is different water, warmer, clearer, with less plankton, and probably less smelt larvae and juveniles.  Smelt are simply tidally-pumped into the central Delta where they are susceptible to warmer, less turbid, predator-laden waters of Franks Tract and the central and south Delta.  Most young smelt probably succumb before reaching the south Delta export pumps.

This is another reason why winter Delta exports need restrictions and why the Franks Tract restoration project with its tide gate on False River needs to proceed as part of the state’s program to recover longfin and Delta smelt.  For more detail on the proposed project see: https://mavensnotebook.com/2019/02/07/bay-delta-science-conference-franks-tract-feasibility-study-applying-the-guidance-of-a-delta-renewed/ .

Figure 1. Franks Tract and False River gage location in west Delta.

Figure 1. Franks Tract and False River gage location in west Delta.

Figure 2. Longfin smelt distribution in March 2020 20-mm Survey #1.

Figure 2. Longfin smelt distribution in March 2020 20-mm Survey #1.

Figure 3. Longfin smelt distribution in March 2020 Larval Smelt Survey #6. Station 901 is in Franks Tract.

Figure 4. False River net daily tidally filtered flow (cfs) in March 2020.

Figure 5. Hourly flow at False River gage March 29 to April 5, 2020.

Figure 6. Hourly water temperature at False River gage March 29 to April 5, 2020.

Figure 7. Hourly turbidity at False River gage March 29 to April 5, 2020.

Figure 8. Hourly chloropyll at False River gage March 29 to April 5, 2020.

Figure 9. Hourly EC at False River gage March 29 to April 5, 2020. Note slightly brackish water (300-500 EC) moves upstream in False River on flood tides (Figure 5), but returns fresher on ebb tide from mixing in Franks Tract.

Increasing Salmon Production in the Central Valley

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The state of California has a comprehensive Water Plan to provide a guide for the state’s future water supply.  Why is there no state Salmon Plan?  California also has a plan to restore Bay-Delta habitat called California EcoRestore.  Why not a SalmonRestore, or at least a comprehensive salmon plan as a part of EcoRestore?

Much of the key to increasing salmon production in the Central Valley is to increase flows in rivers and Delta inflow and outflow.  Another key element is to improve reservoir management for water temperatures and the protection of spawning habitat downstream of dams.  Water in sufficient quantity and of sufficient quality is indispensable.

In addition to better water management, the state needs a plan to implement five basic physical approaches to increasing salmon production in the Central Valley.

  1. Restore River Rearing Habitat – Restore river corridor and side-channel rearing habitat in the mainstem rivers and tributaries
  2. Restore Floodplain Rearing Habitat – Increase volitional access of juvenile salmon to the Valley’s agricultural floodplain through gated weirs; enhance such rearing habitat, and implement strategies to reduce stranding of adult and juvenile salmon in that habitat.
  3. Restore Spawning Habitat – Restore salmon spawning habitat in the mainstem rivers and their tributaries by introducing spawning gravel and improving other physical aspects of channel habitat.
  4. Implement Upstream and Downstream Trap and Haul – Capture juvenile salmonids and transport them from existing spawning areas downstream in dry years when low flows and resulting high water temperatures are unsuitable for volitional downstream migration and survival. Capture and transport adult salmon to upper watersheds above impassable dams, and capture and transport their juvenile progeny back downstream of those dams to locations where high survival is likely.
  5. Increase Hatchery Contributions – Increase the number of hatchery smolts that reach the ocean, while minimizing negative effects of hatcheries on wild salmon populations.

Available options in each of the five categories are virtually limitless, as are the potential costs and benefits.

The National Marine Fisheries Service has a Recovery Plan for salmonid species that are listed as threatened or endangered under the Endangered Species Act.  Such recovery is valuable and important.  But fisheries agencies also can and must do better in supporting the commercial and recreational fishing industries that depend largely on fall-run salmon that are not listed under the ESA.  A state Salmon Plan should be part of the strategy, and the sooner the better.