Category Archives: Bay-Delta

End of May 2016 Smelt Update

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Since my last update in April, Delta and longfin smelt have continued their trends of record low numbers. I opined that they were not yet gone, but close, and that it remained to be seen whether the good conditions provided to date in 2016 could lead to some form of recovery for these two endangered species.  The prognosis remains poor.

Habitat conditions in the Bay-Delta remained good through April and May.  Below normal year estuary inflows were modest, and Delta exports were low thanks to caps in endangered fish species biological opinions.  Longfin and Delta smelt may have further benefitted from a rare spring plankton bloom.

A quick view of the status of smelt can be gleaned by comparing recent May 20-mm Survey results with those from last year, the fourth year of drought conditions, and those from 2010, the last below normal water year before the 2012-15 drought and after the 2007-09 drought.

Longfin Smelt

The May 2016 survey (Figure 1) compares favorably with the 2015 Longfin pattern (Figure 2), but less so with 2010 (Figure 3).  Higher densities of longfin smelt occurred in Suisun Bay this year compared to 2015, although they are generally lower than in 2010.  Year 2010 had higher Delta outflow in spring, and longfin juveniles had a wider distribution and higher densities.

Delta Smelt

The May 2016 survey (Figure 4) shows little or no improvement in Delta smelt compared with 2015 (Figure 5), and poorer performance when compared to 2010 (Figure 6).  Most of the young Delta smelt in 2015 and 2016 were confined to the Sacramento Ship Channel in the north Delta, whereas in 2010 they were more widely distributed into the western Delta and Suisun Bay, albeit in very low densities compared to historical levels.

Map of Longfin smelt young densities from May 2016 20-mm Survey

Figure 1. Longfin smelt young densities from May 2016 20-mm Survey. Source of charts: https://www.wildlife.ca.gov/Conservation/Delta/20mm-Survey

Map of Longfin smelt young densities from May 2015 20-mm Survey

Figure 2. Longfin smelt young densities from May 2015 20-mm Survey.

Figure 3. Longfin smelt young densities from May 2010 20-mm Survey.

Figure 3. Longfin smelt young densities from May 2010 20-mm Survey.

Map of Delta smelt young densities from May 2016 20-mm Survey.

Figure 4. Delta smelt young densities from May 2016 20-mm Survey.

Map of Delta smelt young densities from May 2015 20-mm Survey

Figure 5. Delta smelt young densities from May 2015 20-mm Survey.

Map of Delta smelt young densities from May 2010 20-mm Survey

Figure 6. Delta smelt young densities from May 2010 20-mm Survey.

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.

Rare Bay-Delta Spring Bloom may benefit Smelt

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A rare Bay-Delta spring plankton bloom in 2016 may benefit longfin and Delta smelt (and other fish).  The bloom (a condition in which chlorophyll concentrations consistently exceed 10 micrograms per liter of water) commenced in late April.  Geographically, it extended from Suisun Bay up into the Delta to Rio Vista on the Sacramento River and to near Stockton on the San Joaquin River (Figure 1).

Figure 1. Bay-Delta phytoplankton bloom late-April to mid-May 2016. Plots show chlorophyll concentrations at selected stations from mid-April to mid-May. Source: CDEC.

Figure 1. Bay-Delta phytoplankton bloom late-April to mid-May 2016. Plots show chlorophyll concentrations at selected stations from mid-April to mid-May. Source: CDEC.

The bloom coincided with a drop in previously high early spring Delta inflow and outflow, as well as with low exports and the implementation of San Joaquin River pulse flows.1 Delta outflows were moderate, relatively steady, and higher than in recent drought years, and consistent with a “normal“ year pattern (Figure 2). San Joaquin River pulse flows occurred after mid-April (Figure 3). The Low Salinity Zone or LSZ (0.5-6 ppt) was located in Suisun Bay. X2 (2 ppt) migrated with the tides from Honkers Bay (northwest of MAL) to Sherman Island (northeast of ANH) within eastern Suisun Bay. The head of the LSZ (500-1000 EC) and the bloom extended upstream to Rio Vista on high tides (Figures 4 and 5). Water quality standards (D-1641) that require 14-day average X2 to be at Chipps Island (MAL) or further west helped to ensure consistent Delta outflow.

Longfin smelt concentrated near X2 and may benefit from plankton bloom (Figure 6). Remaining Delta smelt may also benefit as they too concentrate near X2. Maintaining the LSZ and X2 in Suisun Bay is generally thought to promote Bay-Delta productivity and higher smelt survival. In the past four years of drought, the LSZ and X2 during spring and summer have generally been upstream of Suisun Bay, in the Delta.

Figure 2. Delta outflow mid-April to mid-May 2016. Source: CDEC.

Figure 2. Delta outflow mid-April to mid-May 2016. Source: CDEC.

Figure 3. San Joaquin River inflow to the Delta at Mossdale April-May 2016. Source: CDEC.

Figure 3. San Joaquin River inflow to the Delta at Mossdale April-May 2016. Source: CDEC.

Figure 4. Bottom salinity in Sacramento River several miles downstream of Rio Vista in early May 2016. Source: CDEC.

Figure 4. Bottom salinity in Sacramento River several miles downstream of Rio Vista in early May 2016. Source: CDEC.

Figure 5. Chlorophyll concentrations at Rio Vista in early May 2016. Source: CDEC

Figure 5. Chlorophyll concentrations at Rio Vista in early May 2016. Source: CDEC

Figure 6. Catch distribution of young Longfin smelt in late April 2016 along with extent of plankton bloom (red boundary). Smelt were concentrated (larger green dots) near X2 in central and eastern Suisun Bay. Source: CDFW 20-mm Survey.

Figure 6. Catch distribution of young Longfin smelt in late April 2016 along with extent of plankton bloom (red boundary). Smelt were concentrated (larger green dots) near X2 in central and eastern Suisun Bay. Source: CDFW 20-mm Survey.

  1. The bloom also occurred after a winter of moderate Yolo Bypass flood spills that may have contributed nutrients to fuel the bloom. Elevated Bypass flows continued through mid-April. ↩

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.

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.