Author Archives: Tom Cannon

Gross Violation of Water Quality Standards for Water Temperature in Lower Sacramento River Further Degradation of Salmon Habitat

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Water temperatures in the lower Sacramento River over the past month have often exceeded water quality standards that protect salmon and other beneficial uses (Figures 1 and 2).  Water temperatures at or above the standard of 68oF adversely affect adult and juvenile salmon.  Water temperatures can meet the standard if the Bureau of Reclamation maintains flow in the Sacramento at Wilkins Slough at 6000-8000 cfs, depending on air temperature.  The Bureau of Reclamation has maintained such flows in the past to meet water quality standards and terms in its water rights permits (Figure 3).  Shasta Reservoir water storage is 102% of normal as of June 18, 2018.  Water diversions from the Sacramento River upstream of Wilkins Slough are approximately 6,000 cfs, with 100% allocation to CVP contractors under water right permits.  For more on the effects on salmon, see past posts.

Figure 1. Sacramento River flow and water temperature at Wilkins Slough in lower Sacramento River: mid-May to mid-June 2018. Red line denotes water quality standard. Source: CDEC.

Figure 2. Sacramento River water temperature at Verona in lower Sacramento River: mid-May to mid-June 2018. Red line denotes water quality standard. Source: CDEC.

Figure 3. Historical and recent flow at Wilkins Slough. Source: USGS.

2016-2017 Salmon Crash
Sacramento River Fall-Run Salmon Decline

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In an April 2018 post, I revisited the 2007-2009 salmon crash and warned of the current 2016-2017 crash.  In an April 2017 post, I opined on the status of population and its future given the population crashes.  In this post, I update the population data with preliminary estimates of the 2016 and 2017 runs, including (1) the in-river estimate from the spawning grounds between Keswick Dam and Red Bluff (Figure 1), and (2) Coleman National Fish Hatchery (CNFH) and Battle Creek (Figure 2).

I developed a stock-recruitment relationship using the in-river data shown in Figure 1.  A plot of the population-produced from spawners three years earlier (Figure 3) shows extremely poor runs for 2016 and 2017, given the number of parental spawners three years earlier.  The red numbers reflect drought conditions winter-spring of 2014 and 2015, when these broods were rearing and migrating in the Sacramento River in the first few months of their lives.  The earlier posts covered the factors that led to poor survival in the drought years.

Forecasts for the 2018 run are mixed.  Higher jack numbers in the 2017 run likely foreshadow improvements in the adult 2018 run.  Based on the Figure 3 relationships, the higher 2015 run, along with normal year conditions (a green number) for winter-spring 2016 compared to 2014 and 2015, would also indicate an improved run for 2018.   A forecast for 2019 and 2020 runs, given the poor runs in 2016 and 2017, is risky at best, despite reasonably good winter-spring conditions in 2017 and 2018 compared to drought years 2014 and 2015.  A lack of recovery to 2015 spawner levels in the fall 2018 run would be a serious concern.

Figure 1. Run size estimates (escapement) of fall-run Chinook salmon from spawning grounds in the upper Sacramento River between Keswick Dam and Red Bluff from 1975 to 2017.

Figure 2. Run size estimates (escapement) of fall-run Chinook salmon from the Coleman National Fish Hatchery on Battle Creek near Red Bluff from 1975 to 2017.

Figure 3. Spawner-recruit relationship for fall-run in-river estimates of run size from Figures 1 and 2. Number indicates spawner estimate for that year (y-axis) as derived from spawners three years earlier (x-axis). Color indicates winter-spring rearing-migration conditions for that brood (winter-spring 2015 for spawners in 2017). Red denotes dry year in first winter-spring. Green is for normal years. Blue is wet years.

More on the Winter-Run Salmon Decline

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In a March 14, 2018 post, I discussed my long-held theory that the winter-run salmon decline was caused in large part by high fall exports from the Delta that began in the mid 1970s. In this post, I add some further insights on the theory and why it is so important.

First, when the State Water Project came on line in the late 1960’s, potential export pumping more than tripled from 4,400 cfs to 15,000 cfs. In reality, increases in previously low federal fall exports, along with higher state exports, led to much sharper increases in fall exports, particularly in 1975, 77, 80, 82, and 84, coincident with the primary period of winter-run decline from 1975-85. The fall export increase is very evident in the federal export record (Figure 1) and state export record (Figure 2).

Second, the high exports and high salmon salvage observed were not always associated with high Delta inflows. High salvage of winter-run sized juvenile salmon at south Delta export intakes occurred at the end of October 1984 (Figure 3) under low Delta inflow/outflow conditions (Figure 4). This is important because DWR, in its assessment of the WaterFix Project, is maintaining that export restrictions during the first fall and winter flow pulses will be protective of migrating juvenile salmon. But pulse restrictions alone would not be protective.

WaterFix would nearly double the export capacity of the State Water Project. Actual fall exports could increase by 50%, with much of the increase coming from the trio of new North Delta Diversion tunnel intakes that lie directly in the migration path of young winter-run salmon.

Figure 1. Unusually high federal exports occurred in fall 1975, 1980, and 1984 (red circles).

Figure 2 Delta SWP exports in daily average cubic feet per second from 1969 through 1983.

Figure 3. Chinook salmon south Delta export intakes salvage in fall 1984.

Figure 4. Delta inflow from the Sacramento River August 1984 through March 1985.

And then there were none…

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ARE DELTA SMELT FINALLY EXTINCT? HAS THE CANARY SUNG ITS LAST SONG?

In late April and early May 2018, 20-mm Surveys collected no Delta smelt (Figure 1) in the San Francisco Bay-Delta estuary. It’s a new low for Delta smelt since the survey began in 1995, worse even than the 2017 survey catch (Figure 2). The outlook for the population as indexed by the summer and fall surveys looks grim after record lows from 2012-2017. Despite good conditions in spring 2018, the number of adult spawners was too low, indicating a weak recovery potential.

Figure 1. Catch and lengths of Delta smelt collected in the 20-mm Survey in spring 2018. None were collected in surveys 4 and 5

Figure 2. Catch and lengths of Delta smelt collected in the 20-mm Survey in spring 2017.

Pacific Herring and Bay Productivity

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In past posts I have focused on salmon, smelt, sturgeon, and striped bass, even zooplankton, but have yet to discuss Pacific herring. Pacific herring are the Bay-Delta estuary’s most abundant fish and like the other fishes previously mentioned also depend on the estuary for spawning, rearing, or migration. They also support an important commercial fishery in the Bay. 1

Herring larvae and juveniles are also important prey for young salmon and other estuarine and marine fish from winter into summer. Sub-adult and adult herring are key elements of the coastal marine food web of the northern Pacific, from California to Alaska. Herring populations of the northern Pacific, including the Bay’s population, have been generally managed by controlling harvests (usually with quotas or effort limits) and stock-fishery models.2 Like most fish stocks managed by harvest, the populations tend to become overfished with subsequent difficult recovery. The role of the environment in juvenile fish recruitment is often overlooked because it can be very complicated.

Unlike the freshwater spawning smelt, salmon, and sturgeon, herring spawn in coastal marine and estuarine bays including San Francisco Bay, and their larvae move upstream in winter with tidal and estuarine circulation into brackish waters to rear. Some larvae born in San Francisco Bay even drift with tides up into the Delta. Most rear in brackish waters of the North Bay (San Pablo and Suisun bays) feeding on estuarine plankton whose productivity is positively related to freshwater outflow from the Delta and coastal ocean upwelling (enhanced feeding from turbidity and nutrient driven plankton blooms3). When winter storms and associated pulses of freshwater into the Bay are generally common, Bay productivity in winter is generally dependable, as is herring production regardless of the water year type.

However, at some point herring and general Bay productivity will suffer (if not already) if larger portions of freshwater outflow to the Bay are stored in reservoirs or directly diverted for water supply, especially in drier water years. Proposed projects like California WaterFix (Delta Tunnels) and new storage reservoirs will do just that – take more of the water that would normally enter the Bay, especially in drier years with limited runoff to the Bay.

One potential clue about herring productivity is density patterns of larval herring in the winter during peak abundance. Figures 1-4 show February herring densities versus salinity concentration in four recent years of the Smelt Larval Survey. Figure 5 shows long-term trend in Pacific herring densities in April Bay midwater trawl survey. Taking into account biased-low catch in very wet years (1983, 1995, 1996, 1998, 1999), there is a clear downward trend, with very low catch in 2015-2016. With limited data like this it is hard to see real abundance patterns let alone factors that have led to observed differences. There are so many important factors acting together and independently, it is (and will) be hard to determine cause and effect.

Is the pattern in Figures 1-5 a start of a trend of lower densities and more near zero densities in certain areas of the estuary? More analyses and synthesis are needed to answer the question. More science in the form of studies and comprehensive surveys is needed if we are to understand the role of freshwater outflow to the Bay and coastal waters. Is freshwater outflow to the Bay being “wasted” at the expense of human endeavors, or is it a critical element of the coastal ecosystem productivity? I would guess the latter. Pacific herring would be a good ecological indicator or canary in the coal mine, as Delta smelt once were.

Figure 1. Density of Pacific herring in larval surveys of the Bay-Delta versus surface salinity in February 2011, a wet water year.

Figure 2. Density of Pacific herring in larval surveys of the Bay-Delta versus surface salinity in February 2012, a below normal water year.

Figure 3. Density of Pacific herring in larval surveys of the Bay-Delta versus surface salinity in February 2014, a critically dry water year.

Figure 4. Density of Pacific herring in larval surveys of the Bay-Delta versus surface salinity in February 2018, a below normal water year.

Figure 5. Long term trend in Pacific herring average April catch per trawl in stations 100-500s in Bay in Bay midwater trawl survey.