And then there were none…


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

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.

Spring 2018 – Unusual at Best

Flow conditions into and through the Delta are creating an unintended adaptive management experiment this spring. The San Joaquin River is providing half of the 20,000 cfs of Delta inflow. Exports and other water diversions are each taking about 3000 cfs from the Delta, leaving 14,000 cfs for outflow to the Bay. The Delta has been free of salt (Collinsville has been fresh at 200 EC, but salt is now encroaching). These are good conditions for the Delta and the San Joaquin, but horrendous for the Sacramento. Such conditions are highly unusual.

The Bureau of Reclamation’s decision to save water in Shasta reservoir, combined with a low water level in Oroville Reservoir because of ongoing repairs, have led to poor flows and high water temperatures in the lower Sacramento River. Flow at Wilkins Slough on the Sacramento River above Feather River confluence has fallen to 4000 cfs (Figure 1). Flow in the Sacramento River at Verona, below Feather River confluence, is only 7000 cfs (Figure 2). Water temperatures have reached 60°F at Red Bluff and 70°F at Wilkins Slough. Water temperatures above 56°F are detrimental to spawning winter-run salmon near Red Bluff. Water temperatures above 65°F are detrimental to out-migrating juvenile salmon, steelhead, and sturgeon.

A recent increase in releases from Shasta Reservoir is accommodating agricultural diversion demand in the upper Sacramento River below Shasta (Figure 3), while flows decline in the lower river. The increase in the upper river has stimulated emigration of wild juvenile salmon from the upper river, as shown by increased catch at the Red Bluff screw traps (Figure 4). The problem is that two-thirds of river flow is being diverted for Sacramento Valley agriculture, and river temperature rises 10°F along the way. Sacramento River salmon that reach the Delta, along with other Central Valley wild and hatchery salmon, are subject to south Delta exports (Figures 5 and 6). Though south Delta exports have been reduced, their effect remains significant because of low Sacramento River inflow to the Delta.

As I have suggested in past posts, Shasta Reservoir releases should be increased or water diversions from the upper Sacramento River reduced by several thousand cfs, in order to increase lower river flows and reduce water temperatures to no higher than the state water quality standard of 68°F. If this action is not taken, we will simply be feeding most of the young salmon to the abundant stripers that thrive in warm water conditions between Redding and the Bay (Figure 7).

Figure 1. Sacramento River flow at Wilkins Slough in spring 2018.

Figure 2. Sacramento River flow at Verona in spring 2018.

Figure 3. Sacramento River flow below Shasta/Keswick dams in spring 2018.

Figure 4. Catch of juvenile salmon in screw traps, water temperature, river flow, and turbidity near Red Bluff in Sacramento River.

Figure 5. Juvenile Chinook salmon salvage at south Delta export facilities in spring 2018. Red circle outlines recent salvage of wild juvenile spring- and fall-run smolts.

Figure 6. Juvenile Chinook salmon salvage at south Delta export facilities in spring 2018.

Figure 7. Striper limits from late April 2018 guide trip on lower Sacramento River. Source: James Stone.

Spring Hatchery Salmon Releases – Feather River

Hatchery fall-run salmon smolts being released into the Sacramento River at the mouth of the Feather River at Verona on May 2, 2018. SacBee photo.

The California Department of Fish and Wildlife released spring-run and fall-run salmon smolts raised at the Feather River Hatchery into the lower Feather River from late March to early May 2018. The initial spring-run releases were accompanied by a flow pulse up to 14,000 cfs into the lower Feather River.1 The early May release2 of fall-run was made without the benefit of a flow pulse.

Past performance of hatchery spring-run smolt releases is shown in Figure 1. The 2011 successful smolt release was accompanied by 8,000-17,000 cfs Oroville Dam flows (Figure 2) and wet year conditions in the Bay-Delta. The 2012 modestly successful smolt release was accompanied by a 3000 cfs flow pulse. The 2007 to 2009 smolt releases also had an accompanying 3000-5000 cfs flow releases, but flows that followed fell to 1000-2000 cfs. There was no flow pulse in 2010.

The early April 2018 flow pulse in the Feather River was followed by falling flows (14,000 cfs in early April down to 1000 cfs flow in late April – Figure 3). The latest release of fall-run smolts on May 2 was made near the mouth of the river because of low Feather River flows. Flows in the Sacramento River were also low (less than 10,000 cfs – Figure 4), and water temperatures were marginal at 65°F. The evidence summarized in Figures 1 and 2 suggests that smolts should be trucked to the Bay in non-wet years without strong flow pulses. Survival would be further increased if the smolts are barged from the mouth of the river.3

We can expect good survival from the earlier releases that were accompanied by flow pulses and poor survival from the early May release without a flow pulse. The latter release should have been trucked to the Bay.

Figure 1. Survival (% return) of spring-run salmon tag-release groups from 2007-2013 spring smolt releases. Source of data:

Figure 2. Flow (cfs) in the lower Feather River at Gridley in Apr-May 2007-2013.

Figure 3. Flow (cfs) in the lower Feather River at Gridley in Mar-May 2018.

Figure 4. Flow (cfs) in Sacramento River just below mouth of Feather River at Verona in Mar-May 2018.

Delta Smelt Spawning Run – Record Low February 2018 Index

Despite three straight non-drought winters (2016-2018) the Delta smelt spawning run shows no sign of recovery based on the Kodiak Trawl Survey (Figure 1). The February 2018 survey brought a record low catch of only 4 adults (compared to 125-287 from 2011-2013). The March index was “1”. As in my last post, the prognosis for Delta smelt remains grim. The next check is the spring 20-mm Smelt Survey index to determine if this years spawning run production of juvenile smelt continues the pattern of four years of near record lows (Figure 2).

Figure 1. Kodiak Trawl Survey catch of Delta smelt in winter 2002-2018. Source: CDFW survey data.

Figure 2. CDFW 20-mm Survey Delta smelt index 1995-2017. Source: