Category Archives: Water Quality

Bay-Delta Spring Bloom Dissipates

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In a May 17 post I discussed the occurrence of a rare spring Bay-Delta plankton bloom.  The bloom coincided with moderate Delta inflow and outflow in the present “normal” water year combined with a pulse of Delta inflow from the San Joaquin River.  The bloom and associated conditions likely benefitted smelt, salmon, striped bass, and other Bay-Delta fishes by providing cover (turbidity) and food for young fish.

The bloom has now dissipated in the Delta and Suisun Bay (Figures 1-3).  In contrast, the bloom has continued to intensify in the San Joaquin River upstream of the Delta (Figures 4 and 5).  The dissipation of the bloom coincided with the cessation of the San Joaquin pulse flow (2500-3500 cfs from April 18-May 15) combined with Delta inflow and outflow that is increasingly dominated by low turbidity, low nutrient water from the Sacramento River (Figure 6), mainly from high seasonal storage releases from Oroville (Feather River) and Folsom (American River) reservoirs.  In addition, with total South Delta exports now between 2000-3000 cfs, most if not all of the remaining turbid, high nutrient San Joaquin bloom water is being exported before it reaches the central Delta.

This pattern of Delta hydrology in a “normal” Sacramento River water year and a “dry” San Joaquin River water year shows the importance of the nutrient-laden San Joaquin water in the overall productivity of the Bay-Delta estuary.

Figure 1. Chlorophyll concentration May 12-27, 2016 in the lower San Joaquin River channel of the Delta east of Antioch near Sherman Island. Concentrations above 10 micrograms per liter of water are considered indicative of high phytoplankton production – a “bloom”. Source: CDEC.

Figure 1. Chlorophyll concentration May 12-27, 2016 in the lower San Joaquin River channel of the Delta east of Antioch near Sherman Island. Concentrations above 10 micrograms per liter of water are considered indicative of high phytoplankton production – a “bloom”. Source: CDEC.

Figure 2. Chlorophyll concentration April 27-May 25, 2016 in the lower Sacramento River channel of the Delta north of Antioch adjacent to Sherman Island. Concentrations above 10 micrograms per liter of water are considered indicative of high phytoplankton production – a “bloom”.

Figure 2. Chlorophyll concentration April 27-May 25, 2016 in the lower Sacramento River channel of the Delta north of Antioch adjacent to Sherman Island. Concentrations above 10 micrograms per liter of water are considered indicative of high phytoplankton production – a “bloom”.

 

Graph of Chlorophyll concentration April 28-May 27, 2016 in eastern Suisun Bay at Chipps Island near Pittsburg, CA 

Figure 3. Chlorophyll concentration April 28-May 27, 2016 in eastern Suisun Bay at Chipps Island near Pittsburg, CA. Concentrations above 10 micrograms per liter of water are considered indicative of high phytoplankton production – a “bloom”.

Figure 4. Chlorophyll concentration April 28-May 27, 2016 in San Joaquin River upstream of the Delta at Mossdale Bridge.

Figure 4. Chlorophyll concentration April 28-May 27, 2016 in San Joaquin River upstream of the Delta at Mossdale Bridge.

Figure 5. Chlorophyll concentration April 28-May 27, 2016 in San Joaquin River upstream of the Delta at Vernalis.

Figure 5. Chlorophyll concentration April 28-May 27, 2016 in San Joaquin River upstream of the Delta at Vernalis.

Figure 6. The relative proportions of Delta inflow from the Sacramento and San Joaquin rivers in May 2016. The higher proportion of San Joaquin inflow in the first half of May was from a flow pulse. Higher Sacrament River flows after early May are from increased storage releases from Oroville and Folsom reservoirs.

Figure 6. The relative proportions of Delta inflow from the Sacramento and San Joaquin rivers in May 2016. The higher proportion of San Joaquin inflow in the first half of May was from a flow pulse. Higher Sacrament River flows after early May are from increased storage releases from Oroville and Folsom reservoirs.

USBR – Increase Shasta Cold Water Releases

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Water Year 2016 on the Sacramento River has been designated a “Below Normal” year.  Water Year 2010 was also a Below Normal year.  Both years followed multiyear droughts.  In both years, Shasta Reservoir was nearly full at the end of April (2010 was 4.4 maf; 2016 was 4.2 maf).  In early May 2010, Keswick releases were 7500 cfs, and release water temperatures were 50-52°F.  In early May 2016, Keswick releases have been 5200-6200 cfs, and release water temperatures have been 53-55°F.

In April and May, 2010, water temperatures in the upper river remained below 56°F.  In contrast, the warmer, lower flows in 2016 have led to excessively warm water temperatures in the upper Sacramento River.  Water temperatures have reached 60-62°F in the upper river (Figure 1), which are well above the prescribed water quality standard of 56°F necessary to protect spawning salmon and sturgeon.  Winter-run salmon began spawning in late April.  Green and white sturgeon spawn in May.

Figure 1. Water temperature in the upper Sacramento River below Shasta Reservoir in early May 2016. In contrast, water temperatures at these locations during early May 2010 were 56°F or lower.

Figure 1. Water temperature in the upper Sacramento River below Shasta Reservoir in early May 2016. In contrast, water temperatures at these locations during early May 2010 were 56°F or lower.

Reclamation’s CVP operations should strive to maintain the 56°F standard through the spring and summer, as prescribed in the Basin Plan and in the NMFS biological opinion for Shasta operations. This temperature can be achieved by increasing Shasta releases or by lowering the water temperature of releases using the temperature control tower/device (TCD) at the dam, or by a combination of these elements. In the last few days, Reclamation has increased releases and has added colder water, resulting in slightly colder Keswick releases (Figure 1). Reclamation has decreased the temperature of releases by opening one the six middle outlets of the Shasta Temperature Control Device (Figure 2). However, downstream temperatures remain high, because air temperatures and water diversions downstream are also increasing.

While there is some logic behind Reclamation’s decision to minimize reservoir releases to save Shasta storage, it is inappropriate to jeopardize endangered fish in the upper Sacramento River with excessively warm water this year, given the abundance of cold water in the reservoir. 1

With Shasta releases expected to increase soon to meet increasing irrigation demands, it will be imperative that water temperatures upstream of Red Bluff remain below 56°F to protect spawning salmon and sturgeon and their young into and through the summer.

The “official” temperature target and control point since April 15, 2016 have been 58°F at Redding (station CCR). In 2010, the target temperature was 56°F, and the control point was at Jellys Ferry (RM 267), 20 miles downstream of Redding. The State Board and NMFS should immediately change the target temperature to 56°F, and move the control point at least downstream to Jellys Ferry. Preferably, the compliance point should be further downstream at Red Bluff, to be in compliance with the NMFS biological opinion (56°F at Red Bluff – RM 243). The Basin Plan puts the compliance point further downstream still, (56°F at Hamilton City – RM 200). 2

Following catastrophic losses of winter-run in the Sacramento below Shasta during the past two years, it is imperative to meet the summer water temperature goals as prescribed in the NMFS biological opinion. The Shasta cold-water pool and storage available are more than adequate to meet these objectives.

Figure 2. Shasta Dam’s temperature control tower/device or TCD has multiple options for releasing water from the reservoir. One middle outlet was recently opened to reduce the temperature of the water released to the Sacramento River. (Source: USBR MidPacific Division)

Figure 2. Shasta Dam’s temperature control tower/device or TCD has multiple options for releasing water from the reservoir. One middle outlet was recently opened to reduce the temperature of the water released to the Sacramento River. (Source: USBR MidPacific Division)

  1. A disproportionate amount of Sacramento River Delta inflow this spring has come from Oroville Reservoir (Feather River) and Folsom Reservoir (American River) storage releases. Excessive use of Folsom storage to meet Bay-Delta needs could lead to loss of its cold-water pool this summer and greater mortality of over-summering juvenile salmon and steelhead in the American River. ↩
  2. A plan for summer operations from Reclamation is due by May 15, 2016 ↩

Water Quality Standards Optional

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On May 5, I reported on the “chumming of stripers” with the late season release of millions of hatchery smolts into the warm, low flows of the Sacramento and Feather rivers.  So what more could the state and federal managers do to improve conditions for our salmon, steelhead, smelt, sturgeon, and other fish resources?    They could start by obeying and enforcing the rules already on the books.

Because of the restrictions placed on South Delta state and federal water project exports by rules governing San Joaquin River steelhead, exports are now restricted to no more than about 2500 cfs.  Such low exports at this time of year have in fact been the norm for the past 20 years under water quality standards and endangered species biological opinions.  The steelhead biological opinion for the San Joaquin is relatively restrictive this year because of the San Joaquin’s dry-year designation.

So what is the problem?  Because it cannot export, the US Bureau of Reclamation is releasing minimum flows from the warm surface waters of a full Shasta Reservoir.

This causes violations of the standards for Sacramento River water temperature.  The upper Sacramento River standard of 56°F has been violated: water temperatures have been running 60-62°F.  The lower river standard of 68°F has also been violated. water temperatures are running 70-72°F.  These conditions contribute to:

  1. Poor survival adult winter and spring run salmon in their peak migration perio;,
  2. Poor egg survival of winter run in the first month of spawning season;
  3. Poor late fall run salmon fry survival;
  4. Poor sturgeon egg survival during their peak spawning season; and
  5. Poor hatchery and wild smolt survival to the Bay.

The Delta outflow-salinity standard under D-1641 requires salinity at Chipps Island to be no more than 2.64 mmhos on a 14-day running average; the most recent 14-day average is above 3.0 mmhos.  With minimal Sacramento River inflow, Delta outflow has reached as low as 8,000 cfs in early May 2016.  These conditions contribute to:

  1. Poor migratory flows for adult and juvenile fall, winter, and spring run salmon, steelhead, and green and white sturgeon;
  2. Poor longfin and delta smelt survival; and
  3. Poor Delta and Bay productivity.

The standards (rules) governing the Central Valley rivers and Delta are there for a reason: to protect water quality, fish, and ecosystem function.  They do not contain the caveat: ‘Comply when convenient.’  They don’t have an exception that reads: ‘No Exports?  No Problem.  Release what meets your sense of order.’  With such gross disregard for the rules, it is no wonder our fisheries resources are in such a poor state.

Water temperature in past month at Bend Bridge near Red Bluff. Note: in 2010, the last below normal water year, water temperature did not exceed 58°F during first 12 days in May.

Water temperature in past month at Bend Bridge near Red Bluff. Note: in 2010, the last below normal water year, water temperature did not exceed 58°F during first 12 days in May.

River flow in past month at Wilkins Slough below Colusa on middle Sacramento River. Note: flow was 7000-13,000 cfs during first 12 days of May 2010, the last below-normal water year

River flow in past month at Wilkins Slough below Colusa on middle Sacramento River. Note: flow was 7000-13,000 cfs during first 12 days of May 2010, the last below-normal water year

Delta outflow in past month. Note: outflow in the first 12 days of May 2010, the last below normal year, was 20,000-30,000 cfs.

Delta outflow in past month. Note: outflow in the first 12 days of May 2010, the last below normal year, was 20,000-30,000 cfs.

Salmon Fishermen Protest

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The Golden Gate Salmon Association1 and other sport fishing and commercial salmon organizations are protesting the release of Feather River Fish Hatchery salmon smolts into the Feather River near Marysville. In 2016, all four major salmon hatcheries are releasing most of their fall-run salmon smolts into the rivers near the hatcheries. In the drier (and some wet) years of the past two decades, many hatchery smolts have been trucked to the Bay or west Delta and released there after holding in acclimation pens. With higher water releases in this wetter year, hatcheries will now depend on the smolts reaching the Golden Gate in the higher river flows (Sacramento 4500 cfs, Feather 3000 cfs, and American 3000 cfs).

Federal and State fisheries scientists continue to believe it is better to release the fall-run hatchery smolts in the rivers to reduce straying. This logic for this poor management strategy is weak, for the following reasons:

  1. The fall-run stocks are all of the same genetic makeup. Many runs, including those to the San Joaquin tributaries, depend heavily on hatchery fish that have strayed from other rivers. To think that high stray rates of fall-run is the paramount problem is simply crazy. In my own carcass surveys on the Yuba River (no hatchery) and the Cosumnes River (no dam or hatchery), almost all the fall-run were hatchery strays.
  2. Trucking the smolts to the Bay increases survival and fishable stocks in the rivers and the ocean 5 to 10 fold. The socio-economic benefits of salmon fishing depend almost entirely on trucking smolts. Without trucking, ocean and river fisheries will be closed, as occurred during the past decade.
  3. Releasing the smolts in rivers in late April and May is a waste of the resource because only a few percent reach the Golden Gate, compared with 99% that are trucked or barged. The rivers are too warm, even with this year’s higher flows. The Delta remains a black hole for hatchery smolts. Predators are much more active in spring than in the winter, when fall-run naturally migrate through the Bay and Delta. Feather River fall-run hatchery fry stocked in Yolo Bypass rice fields at the beginning of February smolted and emigrated by the first of March.
  4. Releasing smolts in the rivers only encourages and benefits predators, training them to feast in rivers on salmon rather than other normal prey, and increasing growth and survival of predators including birds, striped bass, pikeminnow, and black bass. Stripers now leave their normal habitats in the Bay and Delta for the feast in the rivers. Spawning stripers stay longer in the rivers, feeding on the smolt bounty. A recent video from the Feather River near the hatchery smolt release site shows stripers feeding on hatchery smolts, visual evidence of the negative aspects of the strategy.2 It does not take fishermen long to catch on either.3
  5. The hatchery smolts, including millions of steelhead yearlings, compete with and prey upon wild salmon and steelhead juveniles. The wild late-fall-run salmon in the Sacramento River and all the wild steelhead in the Central Valley rivers are all small fry in spring, and are tasty morsels for the big hatchery smolts.

If straying is such a concern of federal and state fisheries scientists, then why not barge the smolts from the rivers, through the Delta to the Golden Gate, as I have previously suggested?4 Otherwise these scientists should stop wasting tax dollars and license fees of California sport fishermen in the bad practice of releasing hatchery smolts in Central Valley rivers. Furthermore, federal, state and other biologists should quit blaming the problem on stripers that have been around for over a hundred years. Stripers are not as stupid as this hatchery strategy is.

What’s the Plan, Sam?

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Uncle Sam has the Trinity River Plan together for 2016 (Figure 1). Trinity Reservoir is not full (Figure 2) and may not fill, but it is a Wet water year under the Trinity River Record of Decision, and the fish are going to get a lot of water after the worst two storage years since the reservoir first filled in 1963.

I can’t say the same for the other parts of the Central Valley Project in northern California. Despite the fact that Shasta Reservoir will soon fill (4.5 million acre-feet) and is making flood releases, it is only a “Below Normal” year for the Sacramento Valley. But all the north- of- Delta water contractors will be getting 100% of their water allocations. 1

What will the flows be below Shasta? What will be the flows at Wilkins Slough in Sacramento River in mid-Valley? What will Delta inflows, exports, and outflows be? Will the Delta have a wet June? What will the target water temperatures near Redding this summer be for Winter Run salmon? Will it be a 53°F summer target for the salmon for Red Bluff, or will Water Right Order 90-5 requirements be weakened as they has been over the past four years of drought?

The Sacramento River Plan is due at the end of April. It all hinges on whether Shasta will retain 2.2 million acre-ft of storage by the end of September (it will unless diversion demands are excessive). Will the feds and the state try to weaken the standard again? Will they accept poorer results than 2010 and 2011 (Figure 3)?

Figure 1. Trinity River Restoration Program Homepage.

Figure 1. Trinity River Restoration Program Homepage.

Figure 2. Trinity Lake monthly storage level 1962-2016. (Source: CDEC)

Figure 2. Trinity Lake monthly storage level 1962-2016. (Source: CDEC)

Figure 3. Survival of Winter Run year classes below Shasta Dam from 1996-2015

Figure 3. Survival of Winter Run year classes below Shasta Dam from 1996-2015.2 WR 90-05 water temperature standard for Sacramento River near Red Bluff was weakened during 2012-2015 drought. The severely weakened standard in 2014 and 2015 led to poor survival and virtual loss of two year classes.