Category Archives: Smelt

June Update and Possible Solution to 2016 Fish Woes

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Over the past month I related water issues involving Delta and longfin smelt, striped bass, green and white sturgeon, and winter-run and spring-run salmon. All of these species need river flow and cooler water over the next several months. Shasta releases to the upper Sacramento River need to be cold, stable, and sufficient to sustain winter-run salmon eggs in the river near Redding and to sustain moderate flows and cooler water temperatures for 200 miles of river to protect sturgeon and other lifestages of salmon. Sufficient flows needs to pass through the Delta to keep the low salinity zone downstream of the Delta in the cool waters of eastern Suisun Bay, away from Delta exports.

Shasta releases are now 8000 cfs, with Bend Bridge water temperature near the Red Bluff target of 56°F. In June and July of drought years 2012 and 2013, releases were 11,000-14,000 cfs. However, concern over carryover storage and sustaining cold-water releases through summer has led to a more conservative management strategy in 2016. The cold-water pool in Shasta Reservoir is being rationed to make it through the summer. Flows will rise over the next six weeks to 9,000 or 10,000 cfs to satisfy irrigation demands in the upper river.

Flows in the lower Sacramento River at Wilkins Slough need to be greater than 5000 cfs in summer, if only to keep water temperature down closer to the Basin Plan’s 68°F. Flows are now 3000-4000 cfs, with water temperatures up to 75°F. In dry years 2012 and 2013, flows at Wilkins Slough were 6000-9000 cfs, and water temperatures were cooler, as some of Shasta’s storage was allocated for Delta export. This year’s management strategy to hold back Shasta releases will, if continued, keep both Wilkins Slough flows and Delta exports down.

Delta outflows need to be sustained near 10,000 cfs to keep the low salinity zone and X2 (2 ppt salinity) near Collinsville in eastern Suisun Bay. However, July outflow to the Bay required by water quality standards will be only about 8000 cfs. To help save the last of the two smelt species, 10,000 cfs would be far better.

A reasonable solution is apparent: raise Shasta releases through most of the summer by 2000 cfs to 10,000-12,000 cfs and require that the extra release be passed down the river to and through the Delta. While such a management strategy would benefit the fish, it would decrease Shasta storage by 120,000 acre-ft of water per month. At present, Shasta is 90% full at 4.1 million acre-feet (the cold-water pool volume is about 2.4 maf). At 12,000 cfs, the total Shasta release would rise to 600,000 acre-feet per month, which is about the current total release from Oroville (Feather River) and Folsom (American River) reservoirs. NMFS and USBR have determined that a 10,000 cfs Shasta cold-water release can be sustained through the summer, while a 12,000 cfs release could be problematic. Protests would no doubt come from water users who would want the extra 2000 cfs. But note that of the 20,000 cfs being released today from the three main Sacramento Valley reservoirs, only 8000 cfs is reaching the Bay.1

This solution of raising total reservoir releases to 22,000-24,000 and Bay outflow to 10,000 cfs is reasonable to help the fish after four years of drought. In 2014-2015, water quality standards were drastically reduced, with catastrophic effects to fish. The continuing legacy of these catastrophic effects creates the urgency to do better in 2016.

If higher releases from Shasta become problematic for whatever reason, then some compromise should be achievable, noting that water deliveries of Shasta water are to be provided only after the needs of the fish are first considered, including conservation of Shasta’s cold-water pool through the summer and early fall (Water Rights Orders 90-05 and 92-02). Further, Central Valley water rights are provided via the Trinity River trans-basin diversion to Keswick Reservoir on the Sacramento River below Shasta Dam, but the Trinity supply is much in doubt because Trinity storage has failed to recover after the drought, unlike Shasta storage. A lack of Trinity supply this summer will further limit water available for irrigation in the Central Valley. Yet another constraint is whether the available storage in Oroville and Folsom reservoirs is able to satisfy Delta demands without compromising the needs of endangered fish in the Feather and American rivers.

Sorting out these conflicts and needs is the responsibility of the State Water Resources Control Board. The Board’s top priority should be the basic needs of the endangered salmon, sturgeon, and smelts of the Central Valley. At minimum, the Board should require the following conditions this summer:

  1. Below Shasta – Stable flows of 9,000 to 10,000 cfs and 56°F average daily water temperatures near Red Bluff (Jellys Ferry or Bend Bridge).
  2. Lower Sacramento River – minimum 5000 cfs at Wilkins Slough (RM 125 on the Sacramento River)
  3. Delta Outflow – 9,000 cfs in July, 5,000 cfs in August, and 4,000 cfs in September.
  1.  A further complication is that South Delta export criteria allow an increase from 35% of inflow to 65% starting July 1.  Exports in June are limited to 5000 cfs.  In July, exports can be raised to 65% of inflow, but only if outflow is kept at 8000 cfs.  Delta ag diversions are also near 4000 cfs.  Thus July Delta inflow of  20,000 cfs or more (compared to the present inflow of 15,000 cfs) would be needed to allow 10,000 cfs of Delta export.   ↩

It is not too late for Delta smelt

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Before the 2012-2015 drought, Delta smelt had a recovery period in 2010 and 2011. Now, in 2016, there remains an opportunity for some form of recovery, albeit small. What is needed is exactly what the US Fish and Wildlife Service has been pleading for so far this spring to save Delta smelt: more Delta outflow.

This note was at the bottom of the USFWS’s last Delta smelt determination memo to the USBR on June 1, 2016. This literally was their last action this year under the Delta Smelt Biological Opinion because there are no protections in summer once the South Delta reaches a water temperature of 25°C (77°F).

This note was at the bottom of the USFWS’s last Delta smelt determination memo to the USBR on June 1, 2016.1 This literally was their last action this year under the Delta Smelt Biological Opinion because there are no protections in summer once the South Delta reaches a water temperature of 25°C (77°F).

A careful look at the four figures below indicates that there remains a chance to recover smelt this summer. There is a concentration of Delta smelt near Sherman Island in the west Delta (figure 1). If these smelt can get to Suisun Bay in the coming weeks as they did in 2010 and 2011, where habitat is better and where they are away from the influence of the south Delta exports, then they have a chance.

To move the largest remaining concentration of this species in existence downstream, it will take outflows of about 10,000 cfs. Right now outflows are about 7500 cfs (see chart 1, below), the minimum required under present water quality standards. The fisheries agencies and the water projects need to find a way to make up the difference as soon as possible.

Chart 1. Delta outflow in June 2010, 2011, 2015, and 2016. 2011 was a Wet year. 2010 and 2016 are Below Normal water years. 2015 was a Critically Dry year.

Chart 1. Delta outflow in June 2010, 2011, 2015, and 2016. 2011 was a Wet year. 2010 and 2016 are Below Normal water years. 2015 was a Critically Dry year.

Figure 1. Mid-June 20-mm Smelt Survey 2016. Largest green dot is in north side of Sherman Island in Sacramento River channel of west Delta.

Figure 1. Mid-June 20-mm Smelt Survey 2016. Largest green dot is in north side of Sherman Island in Sacramento River channel of west Delta.

Figure 2. Mid June 20-mm Smelt Survey 2010. Note smelt length-frequency chart at bottom-center of chart, which also depicts total caught in survey.

Figure 2. Mid June 20-mm Smelt Survey 2010. Note smelt length-frequency chart at bottom-center of chart, which also depicts total caught in survey.

Figure 3. Mid-June 20-mm Smelt Survey 2011.

Figure 3. Mid-June 20-mm Smelt Survey 2011.

Figure 4. Mid-June 20-mm Smelt Survey 2015. Large green dot is in Sacramento Deep Water Ship Channel.

Figure 4. Mid-June 20-mm Smelt Survey 2015. Large green dot is in Sacramento Deep Water Ship Channel.

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.

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. ↩

Recommendation for 2016 Longfin Smelt Recovery

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In a recent post I suggested possible prescriptions for Water Year 2016 that would help toward recovery of the nearly extinct Delta smelt. In another recent post I also described the probable extinction of longfin smelt.  Both smelt species have suffered considerably in the seven years of drought in the last ten years  due to lack of freshwater outflow from the Delta and excessive Delta exports.

In 2016 longfin smelt should benefit from the same prescriptions for higher outflow and lower exports in similar ways as Delta smelt.  In the past eight years, 2008-2015, Delta outflow is certainly an important factor in longfin survival and production.  In Figure 1 the relationship between the Fall Midwater Trawl Index for longfin smelt and June Delta outflow for the years 2008-2015 shows a strong positive trend.  2010 and 2011 were the wettest two years in the series and had the highest indices and the driest two years; 2014 and 2015, having the lowest.  With 2016 being a “normal” water year similar to 2010, a prescription of 15,000 cfs June outflow would be expected to bring an index closer to 200.  But since Delta standards require at most 7100 cfs outflow, Mother Nature or some other action (e.g., reservoir releases) will be necessary to get June outflow up to the 2010 level.

Figure 1. Longfin smelt Fall Midwater Trawl Index versus June Delta outflow

Figure 1. Longfin smelt Fall Midwater Trawl Index versus June Delta outflow

In reality, what controls longfin production is more than just June outflow.  As described in my previous post, longfin smelt are also suffering from a lack of spawners this year, so there may not be sufficient young-of-the-year abundance this year (see Figure 2) to reach the index level produced in 2010.  Relatively high spring juvenile abundance in 2008 and 2013 failed to produce good fall abundance.  With or without good June outflow, it is unlikely that there will be a good fall index in 2016 because of the depressed population level.  However, that should not preclude a good effort.  Spring abundance was also not extraordinary in 2010 and 2011, but these years still produced improvements in fall longfin abundance.

Figure 2. Catch indices trends for longfin smelt from 2008-2015 in three major Bay-Delta surveys: March 20-mm Survey, June Summer Townet Survey, and Fall Midwater Trawl Survey. (Note: The 20-mm index for March 2016 was 6.)

Figure 2. Catch indices trends for longfin smelt from 2008-2015 in three major Bay-Delta surveys: March 20-mm Survey, June Summer Townet Survey, and Fall Midwater Trawl Survey. (Note: The 20-mm index for March 2016 was 6.)

In its Finding relative to the proposed listing of longfin Smelt, the US Fish and Wildlife Service stated: “Freshwater flow is strongly related to the natural hydrologic cycles of drought and flood. In the Bay-Delta estuary, increased Delta outflow during the winter and spring is the largest factor positively affecting longfin smelt abundance (Stevens and Miller 1983, pp. 431–432; Jassby et al. 1995; Sommer et al. 2007, p. 274; Thomson et al. 2010, pp. 1439–1440). During high outflow periods, larvae presumably benefit from increased transport and dispersal downstream, increased food production, reduced predation through increased turbidity, and reduced loss to entrainment due to a westward shift in the boundary of spawning habitat and strong downstream transport of larvae (CFDG 1992; Hieb and Baxter 1993; CDFG 2009a). Conversely, during low outflow periods, negative effects of reduced transport and dispersal, reduced turbidity, and potentially increased loss of larvae to predation and increased loss at the export facilities result in lower young-of-the-year recruitment. Despite numerous studies of longfin smelt abundance and flow in the Bay-Delta, the underlying causal mechanisms are still not fully understood (Baxter et al. 2010, p. 69; Rosenfield 2010, p. 9).1

Given the depressed state of this species that is listed as threatened under the California Endangered Species Act, it is reasonable to attempt an ambitious prescription this June that has the potential to bring some measure of recovery.