Miracle March/April for Water Supply and Fish

Posted on April 15, 2018 by Tom Cannon

It has been a “Miracle March-April” for water supply and fish in the Central Valley. Over 2 million acre-feet of water was added to Central Valley storage reservoirs. Many major reservoirs reached flood capacity, with large releases and rivers spilling over into flood bypasses. The snowpack doubled to over 50% of average. Water year 2018 cumulative precipitation nearly doubled (remains 10 inches short of average at about 80% of normal).¹ Water Year 2018 will likely stack up as “below normal,” not unlike 2010, 2012, or 2016.

Without the added precipitation so far this spring, water conditions would be similar to critically dry 2015. The prognosis for salmon, smelt, and sturgeon would be poor with yet another drought year. The fish have yet to recover from the 2012-2016 drought.

In the next three months, tens of millions of wild and hatchery juvenile salmon and steelhead will be leaving Valley rivers for the Delta, Bay, and ocean. Millions of young smelt and sturgeon will be trying to reach their Bay low salinity nurseries. Adult fall, winter, and spring run salmon and green and white sturgeon will be seeking their upriver spawning grounds. All of these populations are in real trouble and need help after years of stress.

Some of the Miracle March-April water added to Central Valley storage should be set aside for the fish. Fish need higher river flows and Delta outflow through summer than would normally be allocated in a sub-normal water year like this. Lower Sacramento River flows (Figure 1) should be kept near 8000 cfs, not the projected 5000-6000 cfs. San Joaquin River flows should be kept near 1000 cfs (Figure 2). The Delta outflow minimum should be 8000 cfs (Figure 3), not 5000 cfs, by allowing the added river flows to pass through the Delta. The “extra” water would amount to about a quarter of Mother Nature’s gift to the reservoir supply added so far this spring. That would seem more than reasonable and fair. In most cases it means meeting already prescribed flow and water temperature standards for the Central Valley rivers and Delta. These standards have been more than regularly ignored in recent years. So let’s do the fish a favor for once – call it “adaptive management” – and see if it helps.

Figure 1. Flow in lower Sacramento River at Wilkins Slough over past decade.

Figure 2. Flow in lower San Joaquin River at Vernalis over past decade.

Figure 3. Delta outflow at Pittsburg over past three years.

https://mavensnotebook.com/2018/04/02/reservoir-and-water-conditions-for-april-2nd/#jp-carousel-74454 ↩

San Joaquin River Spring-Run Salmon at Risk

Posted on April 11, 2018 by Tom Cannon

Give them a chance.

Soon after spring run salmon smolts were released from the new San Joaquin River Spring-Run Recovery hatchery at the beginning of March, they began appearing in south Delta export salvage facilities (Figure 1). The number salvaged is unusually large, about one percent of the 87,000 released¹, in salvage historical records as indicated in Figure 1. The salvage rates of recovery for the other winter 2018 Central Valley hatchery releases are much lower. The high rate of salvage of the March 1 San Joaquin River spring-run release reflects the vulnerability of young salmon that are drawn into the south Delta, where they are at risk to the State Water Project (SWP) and Central Valley Project (CVP) export facilities.

That risk comes from high export levels in winter-spring. Salvage of the spring-run smolts increased sharply as combined SWP and CVP exports reached high levels (8000-10,000 cfs) in late March (Figure 2). Such high exports were allowed this spring because of the increase in San Joaquin flows in late March (Figure 3). Tying export limits to San Joaquin flows² and OMR flows is obviously not protecting San Joaquin salmon emigrants. The flow pulse may be the trigger that moves the young salmon down to the Delta. Exports should be reduced, not increased, during such pulses. But both current requirements as prescribed in the OCAP Biological Opinion for the Delta operations and requirements proposed under WaterFix allow increasing exports as flows increase.

Figure 1. Salvage of salmon at south Delta export fish facilities August 8, 2017 to April 5, 2018.

Figure 2. Salmon salvage and export rates from state and federal export facilities in south Delta March 1, 2018 to April 5, 2018.

Figure 3. San Joaquin River flow at Mossdale December 10, 2017 to April 7, 2018.

Note: the actual rate of tagged fish recovered is much higher because salvage numbers are estimated from subsamples, and many fish are lost in Clifton Court Forebay prior to reaching salvage facilities. ↩
Exports are also limited by Old and Middle River negative flow limits (-5000 cfs), which were exceeded in late March ↩

Where have all the salmon gone?

Posted on March 25, 2018 by Tom Cannon

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

Posted on March 21, 2018 by Tom Cannon

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

Posted on March 14, 2018 by Tom Cannon

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.