Category Archives: Bay-Delta

Where have all the salmon gone?

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Based on early indicators, it appears that salmon populations in the Central Valley are in critical condition. First, there was poor smolt production from the 2014 and 2015 drought-year salmon runs in the Central Valley. That led to last fall’s (2017) runs being so poor that Coleman Hatchery had to get eggs from state hatcheries on the Feather and American rivers to meet its needs.1 CDFW believes poor ocean conditions have led to low adult salmon numbers for 2018 fisheries and runs. The weak runs may eliminate 2018 salmon fisheries. 2

The evidence based on initial surveys is that brood year 2017 salmon (born last summer and fall) fry-smolt production was extremely poor. First, lower Sacramento River screw trap catches are low in early 2018 compared to 2017 (Figures 1 and 2). Winter screw trap catch-per-trap-day (and Sacramento trawl catch not shown) in the lower Sacramento River in 2018 are only 2% of 2017. Note flows and turbidities were very low in 2018 compared to 2017. I warned that these conditions with warmer water would lead to slower migration rates, starvation, and high predation by stripers. Second, salmon salvage at the south Delta pumping plants has been extremely low in 2018 (Figure 3) compared to 2017 (Figure 4). Salvage is a strong indicator of relative abundance. Third, compared to historical levels (Figure 5), salvage numbers in 2018 are two orders of magnitude lower than in 1999 when salmon runs were last strong.

You can blame the problem on the 2012-2016 drought, poor ocean conditions, or poor river-Delta flow management as I do. Whatever the cause, strong measures are needed to recover the salmon populations. Without strong measures, future brood year production will be so low there will be few salmon and no salmon fishing.

Figure 1. Knights Landing screw trap catch Aug 2017 to Mar 2018.

Figure 2. Knights Landing screw trap catch Aug 2016 to Aug 2017.

Figure 3. Chinook salmon salvage at CVP fish facilities in south Delta Nov 2016 to March 2018, along with export rate at Jones Plant. Note very small, nearly unperceivable numbers in winter 2018.

Figure 4. Chinook salmon salvage at SWP fish facilities in south Delta Nov 2016 to March 2018, along with export rate at Clifton Court. Note very small, nearly unperceivable numbers in winter 2018.

Figure 5. Chinook salmon salvage at CVP and SWP fish facilities in south Delta Jan 1999 to June 1999, along with export rate at south Delta pumping plants.

Delta Zooplankton

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One never hears much about Delta zooplankton, the food of most of the pelagic fish including smelt, and also the food of shad, young striped bass, and even young salmon. Zooplankton are the heart of the Delta foodweb. For decades, surveys by CDFW and others have noted that zooplankton suffer in droughts, as do fish that feed upon them. I (and many others) have always believed that zooplankton were one of the key factors in Delta pelagic fish declines. Many science papers suggest shifts in species composition over decades and declining densities after clam invasions as being key factors in long term trends in zooplankton. Rarely are freshwater inflow/outflow or Delta exports offered as key factors in zooplankton trends.

The multi-decade Bay-Delta zooplankton survey database is large and complex, making analyses difficult and time-consuming. There are no indices to follow abundance patterns as there are for fish.

In this post, I provide some insights using a few specific comparisons of zooplankton densities between 2015, a drought year, and 2017, a wet year. I focus on spring and early summer, when zooplankton are perhaps at their greatest importance as fish food and when the difference between year-types is usually greatest.

Some example comparisons are presented in charts below. Figure 1 depicts the difference in May between 2015, a critically dry year, and 2017, a wet year, for Cladocera (commonly referred to as water fleas), a predominantly freshwater zooplankton and important pelagic fish prey. Figure 2 depicts differences between June 2015 and 2017 densities of Pseudodiaptomus, a key young smelt food. Figure 3 depicts differences for total copepod nauplii in July. In each figure, the location of the low salinity zone is referenced by the X2 factor.

My interpretation of all this is that zooplankton abundance and thus pelagic fish production are controlled by (1) flows through the Delta, (2) the location of the low salinity zone, and (3) south Delta exports. A much greater proportion of these key zooplankton populations are highly vulnerable to south Delta exports in drier years with low flows. Furthermore, the proposed WaterFix would exacerbate these conditions and contribute further to the decline of Bay-Delta fish, primarily by reducing spring flows in the northern Delta channels and shifting the low salinity zone eastward. WaterFix would be less ofa factor in summer as south Delta exports are likely to predominate.

Figure 1. Comparison of Cladoceran densities in May plankton surveys in 2015 and 2017, critical dry year and wet years, respectively. Red line denotes X2 (~3800 EC) in center of low salinity zone. Note that cladocera distributed further downstream in wetter 2017.

Figure 2. Comparison of Pseudodiaptomus copepodid densities in June plankton surveys in 2015 and 2017, critical dry year and wet years, respectively. Red line denotes X2 (~3800 EC) in center of low salinity zone. Note higher densities and distribution further downstream in wetter 2017.

Figure 3. Comparison of copepod nauplii densities in July plankton surveys in 2015 and 2017, critical dry year and wet years, respectively. Red line denotes X2 (~3800 EC) in center of low salinity zone. Note higher densities and distribution further downstream in wetter 2017.

Winter-Run Chinook Salmon – What Really Caused Their Decline

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The winter-run Chinook salmon population crashed around 1980 and has not recovered (Figure 1). The population started coming back from 2001-2006 but fell to 827 in 2011. It remained in the 1500 to 6000 range from 2012-20161 with the help of the Livingston Stone federal hatchery near Redding. Hatchery fish make up an increasing proportion of the population each year.

In a 2011 review, NMFS attributed the general population decline to “blockage of access to historic habitat, other passage impediments, unscreened water diversions, heavy metal pollution from mine runoff, disposal of contaminated dredge sediments in San Francisco Bay, ocean harvest, predation, drought effects, juvenile losses at the CVP and SWP Delta pumping facilities; and elevated water temperatures in spawning grounds.”  Droughts and the loss of cold water pool in Shasta are generally considered the primary cause of the decline over the past four decades starting with the 1976-1977 drought.  The decline continues despite “reduced harvest impacts, Iron Mountain Mine clean up, screening of water diversions, altered CVP water operations that improve passage and reduce predation, and construction of a temperature control device on Shasta Dam”. 

A range of actions is being implemented to help recover this NMFS-designated “Species in the Spotlight.”  The problem is the actions do not include the one key factor that was a major cause of the original decline and the primary cause of the lack of recovery:  high late-fall and early-winter Delta exports cause high juvenile salmon mortality in the Delta.

The problem starts from the fact that winter-run juveniles leave the upper Sacramento River rearing area for the Bay-Delta and eventually the ocean with the first fall or early winter rains that produce flow pulses from undammed Sacramento River tributaries.  These same untamed flows are also a primary target of the state and federal export facilities in filling south-of-Delta storage depleted from the summer.  Delta exports have few restrictions in fall.  The allowed export-to-inflow ratio is 65% (compared to 35% in winter-spring).  There are no OMR limits.  Interior Delta flows caused by high exports reach -10,000 cfs, compared to -5000 cfs in winter-spring.  The Delta Cross Channel is usually open through the fall and closed in winter, allowing salmon to move from the Sacramento River to the interior Delta more easily in fall.  Higher fall exports are also a consequence of increasing winter-spring protections (in water quality control plans and endangered fish biological opinions) for fish that led to reduced exports in those seasons.  Fundamentally, higher fall exports were a result of the state export facilities coming on line in the mid-1970s, which increased the export capacity from 4,400 cfs to 15,000 cfs.

One need only look at the increase in fall export rates and juvenile salmon salvage in the south Delta to see the association with the decline of winter-run.  Figure 2 shows CVP exports in 1984-1985 compared with the historical average.  Figures 3 and 4 show fall exports in the example years.  Figure 5 shows fall 2016 exports and Delta inflow, which is compelling proof that the problem continues.2  Figure 6 shows high negative Old and Middle River (OMR) flows caused by high exports.  Figure 7 shows December Chinook salmon salvage at south Delta fish facilities.  Further evidence of the association between fall exports and the decline of winter-run is available in the long-term fish salvage data that dates back to the 1970s historical period depicted in Figure 1.  Further discussion on the risk of high fall and early winter risks to salmon from exports is presented in http://calsport.org/fisheriesblog/?p=1949 .

Figure 1. Trend in winter-run salmon escapement to the Sacramento River below Shasta Reservoir 1970-2009 in thousands of adult salmon. Source

Figure 2. Tracy (federal) export rate in 1984-1986, with mean daily export rate 58-year average. Note marked increase in Nov-Dec period over historical average.

Figure 3. Federal and state export rates in fall 1984.

Figure 4. Federal and state export rates in fall 1985.

Figure 5. Delta export and inflow rates in fall 2016.

Figure 6. OMR December 2016.

Figure 7. Chinook salvage fall 2016.

  1.  https://nrm.dfg.ca.gov/FileHandler.ashx?DocumentID=84381 ↩
  2. Exports were greater than 10,000 cfs from 11/19/17 to 12/8/17. ↩

Measures to Save the Delta and Delta Smelt

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The key to saving the Bay-Delta Estuary and its native fish community is keeping the Low Salinity Zone (LSZ) and its brackish water out of the Delta, especially the south Delta where the federal and state project pumps are located.  The native fish of the estuary, both in the Bay and Delta, depend on potency or productivity of the LSZ.  Much research has shown that low Delta freshwater outflow allows the LSZ to move into the Delta, to the detriment of overall ecological productivity and of the survival and production of native fish (and most pelagic species and their food supply).  Allowing the LSZ to move into the Delta allows the export of the LSZ from the south Delta, to the detriment of native fish and their critical habitats.  Increased salinity also harms agricultural and municipal water supplies.

Keeping the LSZ out of the Delta means keeping salinity (as measured by electrical conductivity or EC) below 500 EC.  The 500 EC level is sometimes called the “salt front” or the upstream head of the LSZ.  Another measure of the LSZ is X2, the heart of the LSZ, approximately 3800 EC.  The State Board has defined the Emmaton gage on the Sacramento River channel and Jersey Point gage on the San Joaquin River channel as the western edge of the Delta in terms of Delta agriculture and set wet year standards of a maximum 500 EC for the spring to fall irrigation season.  These standards have kept the LSZ out of the Delta in summer of wet years to the benefit of Delta agriculture and native fishes (and non-native striped bass).  However, the standard is also needed in the non-irrigation season when high Delta exports often occur.

Suggested measures to save the Delta:

  1. Do not allow south Delta exports to exceed a minimum (often prescribed as 1500 cfs) when Jersey Point and Emmaton gages exceed 500 EC.
  2. Place barriers on False River and Dutch Slough channels when their gages may exceed 500 EC.
  3. Open the Delta Cross Channel (DCC) to maintain a balanced EC at the Jersey Point and Emmaton gages and ensure positive outflow from the Delta at Jersey Point (often referred to as a positive QWEST). Closure of the DCC when EC rises at Jersey Point is detrimental to the LSZ when south Delta exports exceed 1500 cfs.
  4. Restrict Old and Middle River (OMR) negative flows to protect salmon and smelt from export facilities when these fish are in the interior Delta under freshwater conditions per biological opinions.
  5. Install or construct a permanent Head of Old River Barrier to keep San Joaquin salmon out of the south Delta in winter-spring under all export conditions.
  6. Increase San Joaquin River flows in the February-June time period.
  7. Keep Delta outflow at 8000-10,000 cfs in the fall after wet years to keep salt out of the Delta.

Example:  Water Year 2018

This new water year with its record November (wet) and December (dry) is a good example of what is wrong with the Delta.  Despite high reservoir levels for the beginning of a new water year1, Delta outflow was allowed to fall to 5000-7000 cfs in late November (Figure 1) as Delta exports literally sucked the freshwater bubble out of the Delta.  Exports averagedover 10,000 cfs from mid-November to mid–December, a time of year when there are no Delta controls.  The LSZ encroached at Emmaton (Figure 2), Blind Point (Figure 3), False River (Figure 4) on the west side of the Delta, Dutch Slough (Figure 5), and even showed up at the Rock Slough intake of the Contra Costa Water District in the south Delta (Figure 6).  See Figure 7 for the gage locations.

In conclusion, maintaining the 10,000 cfs Delta outflow necessary to keep the salt out of the Delta this past fall would have cost approximately 250,000 acre-ft of water from either the 18,000,000 acre-ft in storage or 1,500,000 acre-ft of Delta exports.  Doing so would have gone a long way toward protecting the past year’s production of winter-run smolts and pre-spawn Delta smelt that were both concentrated in the Delta.

Figure 1. Daily average Delta outflow for 11/7/17 to 1/4/18. Note each box-cell in chart represents approximately 7000 acre-ft of water. Maintaining a target 10,000 cfs to keep salt out of the Delta would have required an additional approximately 250,000 acre-ft of storage releases or export reduction.

Figure 2. The LSZ has encroached into the Sacramento River channel of the western Delta increasingly this water year. The limit should be 500 EC.

Figure 3. The LSZ has encroached into the San Joaquin River channel of the western Delta increasingly this water year. The limit should be 500 EC.

Figure 4. The LSZ has encroached into the central Delta via the False River channel from the western Delta increasingly this water year. The limit should be 500 EC.

Figure 5. The LSZ has encroached into the central and south Delta via the Dutch Slough channel of the western Delta increasingly this water year. The limit should be 500 EC.

Figure 6. The LSZ has encroached into the central and south Delta as seen at the Rock Slough gage of the south Delta increasingly this water year. The limit should be 500 EC.

Figure 7. Location of gages in above figures.

  1. As of December 1, Sacramento watershed reservoirs were 109% of average, and San Joaquin reservoirs were 150% of average. ↩

Delta Smelt: End of 2017

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In a recent post, I summarized the population dynamics of Delta smelt using the Summer Townet Index and Fall Midwater Trawl index relationships.  Since then, the California Department of Fish and Wildlife updated the Fall Midwater Trawl Index for 2017.  In turn, I update the relationships in Figures 1 and 2 below.  As I predicted in another post last fall, there was no uptick in the 2017 index, despite it being a wet year.  News articles on the subject suggest “no easy answers.”  To me it is obvious that the water project managers went out of their way to short smelt in 2017.  The prognosis for Delta smelt remains grim.

Figure 1. Log vs Log plot of fall FMWT Index of Delta smelt as related to the prior summer STN Index of abundance for that year. Blue years are wet water years (Oct-Sept). Green years are normal water years. Red years are dry and critical water years. Year types are as determined by the California Department of Water Resources for the Sacramento River runoff to the Bay-Delta Estuary (http://cdec.water.ca.gov/cgi-progs/iodir/WSIHIST).

Figure 2. Log vs Log plot of fall FMWT Index of Delta smelt (recruits) vs previous fall index (spawners). Blue years are wet water years. Green years are normal water years. Red years are dry and critical water years. Year types are as determined by the California Department of Water Resources for the Sacramento River runoff to the Bay-Delta Estuary (http://cdec.water.ca.gov/cgi-progs/iodir/WSIHIST).