Welcome to the California Fisheries Blog

The California Sportfishing Protection Alliance is pleased to host the California Fisheries Blog. The focus will be on pelagic and anadromous fisheries. We will also cover environmental topics related to fisheries such as water supply, water quality, hatcheries, harvest, and habitats. Geographical coverage will be from the ocean to headwaters, including watersheds, streams, rivers, lakes, bays, ocean, and estuaries. Please note that posts on the blog represent the work and opinions of their authors, and do not necessarily reflect CSPA positions or policy.

Washington State increasing hatchery salmon production Major realignment toward wild population recovery

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Washington State is increasing salmon production to help in recovery of near extinct salmon populations and orca (killer whales). A Washington state Department of Fish and Wildlife webpage describes the role of hatcheries in restoring wild salmon stocks:

In recent years, state hatcheries also have taken on an equally important role in helping to recover and conserve the state’s naturally-spawning salmon populations. Nearly all the hatcheries in the Columbia River and a number of hatcheries in Puget Sound play a role in wild fish rebuilding programs, whether by rearing juveniles prior to release or holding fish through their lifespan to ensure the survival of depressed stocks. This renewed focus on wild stock recovery represents a major realignment in hatchery operations, as WDFW, the tribes, federal government and independent scientists worked to develop a comprehensive operations strategy for hatcheries in Washington. 1

The main reform actions being taken in Washington’s program are:

  1. Marking all hatchery salmon smolts allows identifying hatchery fish by hatchery and lot group. It also allows mark-selective fisheries that require release of wild salmon.
  2. Developing salmon population-specific recommendations intended to provide scientific guidance for managing each hatchery more effectively in the future.
  3. Keeping hatchery program budgets in pace with increasing operating costs (especially utilities, fish feed and labor costs), and not forcing cutbacks in some programs.
  4. Updating aging hatchery infrastructure.
  5. Supplementing wild stocks: to maximize egg fertilization and fry survival (of wild) and thereby increase the number of “wild-type” smolts heading out to the ocean.
  6. Maintaining captive broodstocks of endangered stocks with dangerously low population levels: juveniles are maintained in a hatchery for their entire life to ensure the stock’s survival.
  7. Minimizing interaction between naturally-produced and hatchery-produced outmigrating juveniles and adult fish returning to streams to spawn where necessary.
  8. Donating surplus adult salmon from hatcheries to non-profit hunger-relief programs.
  9. Introducing hatchery carcasses or analogs back to streams to increase natural productivity to low productivity streams.

While California is slowly moving toward some of these reforms, there is resistance to others. For more information and links on California hatchery programs see http://calsport.org/fisheriesblog/?cat=5 , https://www.wildlife.ca.gov/fishing/hatcheries , http://cahatcheryreview.com , https://www.fws.gov/sfbaydelta/Fisheries/hatcheries/NoCAHatcheriesUSFWS.htm .

 

Late-Fall-Run Salmon Update Record low runs in fall 2015 and 2016

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In an April 2017 post, I related factors likely important to late-fall-run Chinook salmon in the reach of the Sacramento River downstream of Shasta Reservoir. In this post, I update that assessment with 2015 and 2016 escapement estimates and coded-wire-tag return data from Coleman Hatchery smolt releases from brood years 2008-2013.

Late-fall-run Chinook salmon escapement reached new lows in 2015 and 2016 (Figure 1). The adult returns in these two years were the product of spawning in brood years 2012 and 2013 and of early rearing conditions in winter of 2013 and 2014 (critical drought years).

Figure 1. Late-fall-run escapement 2000-2016. Escapement refers to adult run counts beginning in late fall of spawning year. For example, 2016 represents late-fall-run for water year 2017 (Oct16-Sep17). Source: CDFW Grandtab.

The low escapement in 2015 and 2016 is also reflected in the spawner-recruit relationship (Figure 2).  There is a continuing significant positive spawner-to-recruit relationship and even stronger effect of water-year type, with poorer recruitment from dry-year winter rearing conditions.

The low 2016 escapement is likely in part a consequence of a very poor return from brood year 2013 hatchery smolts (Figure 3).  Of the approximately one million smolts tagged and released in 2014 at the Coleman hatchery near Redding, less than a tenth of a percent survived to be counted in fisheries and escapement surveys.  A good survival rate would be 1 to 3 percent, as occurred for brood year 2010 (2013 run).

Hatchery and wild smolts from brood year 2013 had poor flow conditions in early winter of 2014 (Figure 4), while brood year 2010 had the best flow conditions.  There were no flow pulses to help the smolts move the 200 miles down to the Bay-Delta in January 2014.

The fact that few late-fall smolts showed up in south Delta salvage in 2014 (Figure 5), compared to higher salvage in 2013 (Figure 6), is compelling evidence that smolt survival to the Delta was very poor in 2014.

Conclusion:  To sustain the late–fall-run salmon population, higher winter flows and flow pulses are warranted in the lower Sacramento River in drier years.

Figure 2. Spawner-recruit relationship for late-fall–run salmon. Number is log10-1.5 transformed escapement (recruits) for the fall of that year. For example, year “16” represents escapement for late fall 2016, which includes spawners from early winter 2017. Spawners represent escapement from three years earlier (brood year). In the example, spawners for year 16 were the progeny of escapement in 2013. Colors represent winter rearing condition two years earlier. In the example, red “16” represents dry winter 2014. Green represents normal years two years earlier. Blue represents wet years two years earlier.

Figure 3. Hatchery smolt survival for brood years 2008-2013 based on coded-wire-tag returns.

Figure 4. January river flow at Wilkins Slough in lower Sacramento River 2009-2014. Note very low flows and lack of flow pulses in January 2014.

Figure 5. Salvage of salmon at the Delta pumps in water year 2014. Note only one late-fall tagged smolt (yellow dot), collected in March after January release.

Figure 6. Salvage of salmon at Delta pumps in water year 2013. Note many late-fall tagged smolts salvaged (yellow dots) beginning in December, coincident with flow pulses after December and January releases of hatchery smolts.

 

Longfin Smelt End of 2018 A Case for Higher Delta Outflow Standards in June

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In a February 2018 post I last updated the status of longfin smelt in the Bay-Delta. I showed that longfin smelt have a strong spawner-recruit or stock-recruitment relationship wherein new recruits into the population depend on the abundance of spawning parents (Figure 1). The relationship also indicated a strong influence of water–year type.

What is it in wetter years that improves survival? What is it about wet years that is important to longfin survival? My analysis is it is the spring Delta outflow, with June likely being important. The fall longfin index is significantly correlated with June outflow (Figure 2). It requires Delta outflows in the 8000-10,000 cfs range to keep the low salinity zone and young longfin in the Bay, west of the Delta and away from the south Delta export pumps and warm low-productivity pelagic habitats.

Present standards (see link, pdf pages 26-27) for June require outflow of 7100 cfs on a 30-day running average. This contrasts sharply with previous June standards under Water Rights Decision 1485 (see link, pdf page 43) which required an average monthly flow of 9500 cfs in some below normal years, 10,700 cfs in Above Normal years, and 14,000 cfs in Wet years. In its ongoing update of the Bay-Delta Plan, the State Water Resources Control Board must account for the importance of the outflow standard for June in protecting Bay-Delta ecological resources.

Figure 1. Longfin Recruits (Fall Midwater Trawl Index) vs Spawners (Index from two years prior) in Log10 scale. Wet years in blue. Dry years in red. Note the progressive decline in recruits in the last three wet years (06, 11, 17). The relationship is very strong and highly statistically significant. Taking into account Delta outflow in winter-spring makes the relationship even stronger. Recruits per spawner are dramatically lower in drier, low-outflow years (red years). Source: http://calsport.org/fisheriesblog/?p=1360.

Figure 2. Fall midwater trawl index for longfin smelt versus average June outflow (cfs) 2008-2017. Wet years in blue. Normal years in green. Dry years in red. Source of data: http://www.dfg.ca.gov/delta/data/fmwt/indices.asp?view=single.

 

Summer Delta Salinity Standards: 2018 Example

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In a July 2016 post I recommended a 500 EC (electroconductivity) salinity standard from July-to-mid-August for the western Delta. The longstanding Water Rights Decision 1641 standard includes this only in Wet years. It should apply in all year types unless south Delta exports are at minimum levels.

In summer 2018, a Below Normal, subnormal snowmelt year, Jersey Point salinity was kept near 500 EC through early August (Figure 1) instead of the allowed 740 EC. Was this an adaptive management experiment? If so what benefits were derived from the experiment?

Figure 1. Jersey Point salinity (EC) remained near 500 EC in early summer 2018. The applicable standard was 740 EC 14-day average through August 15.

Benefit #1:
The water temperature in the west Delta in 2018 was kept near 73°F or below (Figure 2), a good thing. In 2016, the previous Below Normal year, EC was allowed above 500 EC (Figure 3) per the existing standard. Water temperature exceeded 73°F to near 75°F (Figure 4), a bad thing, when EC exceeded 500. The reason for the higher early summer 2016 EC and warmer water temperatures was low Delta outflow (Figure 5). Outflow in 2016 was about 7000 cfs, but needed to be near 8000-9000 cfs. In 2018, outflow in late June was 7500-7900 cfs (Figure 6), in part due to relatively low early summer Delta exports (Figure 7) compared with 2016 (Figure 8).

Other Benefits:
It is really too bad that we can no longer look to Delta smelt for response to adaptive management. But I suspect positive response to the 2018 “experiment” occurred in survival of other juvenile Delta fish (e.g., striped bass), shrimp, zooplankton, and phytoplankton. When 2018 data become available, the comparison with 2016 and prior years can be made.

Conclusion:
The salinity standard for the west Delta at Jersey Point and Emmaton should be 500 EC daily average unless south Delta exports are restricted to minimum health and safety levels. The standard should be year-round in all year types. Delta exports should be restricted to the minimum unless the salinity standard is met.

Figure 2. Water temperature at Jersey Point in west Delta summer 2018.

Figure 3. Jersey Point salinity EC summer 2016. Standard was 740 EC 14-day average through August 15.

Figure 4. Water temperature at Jersey Point in west Delta summer 2016.

Figure 5. Delta outflow in summer 2016.

Figure 6. Delta outflow in summer 2018.

Figure 7. State exports from south Delta summer 2018.

Figure 8. State exports from south Delta summer 2016.

 

Fall Pulsed Flow Protections for Winter Run Salmon Not in 2017 and 2018

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It is well known that juvenile winter-run salmon migrate downstream to the Delta from their upper Sacramento River rearing area near Redding/Red Bluff with the first fall-winter flow pulses.1 Protection of this critical migration of winter-run has been recommended in recent Delta proceedings. In the WaterFix petitions process at the State Water Resources Control Board, such protection is referred to as “pulse protection.” So based on the importance of protecting winter-run during this key life-history stage, one would think such protection would have been applied in the fall of our most recent wet year 2017 and below-normal 2018. A quick check of the facts indicates otherwise.

In 2017, the initial pulse of juvenile winter-run salmon passed Red Bluff (rivermile 240) during September and October, prior to any flow pulses (Figure 1). The first major pulses of flow occurred in the latter half of November 2017. A migration spike of winter-run-sized smolts at Knights Landing screw traps (rivermile 90) did occur during the flow pulse (Figures 1 and 2). Instead of protecting these winter run as they were entering the Delta, south Delta exports were increased to take advantage of the available inflow (Figure 3). The increase occurred with the Delta Cross Channel partially open (Figure 4), increasing the risks of migrating salmon to south Delta exports. Other than a four-day pulse, Delta outflow generally declined before and after the flow pulse (Figure 5). Salinity in the lower Sacramento and San Joaquin Delta channel generally increased with the higher exports and lower outflows (Figures 6 and 7).

In 2018, the initial pulse of juvenile winter-run passed Red Bluff in September and October prior to flow pulses (Figure 7). The first major pulse of flow occurred at the end of November. A migration spike of winter-run-sized smolts at Knights Landing screw traps occurred during this flow pulse (Figures 7 and 8). Instead of protecting these juvenile winter run as they were entering the Delta, south Delta exports were increased to take advantage of the available inflow, with nearly two-thirds of the Delta inflow being exported (Figure 9).

The lack of protection is likely a consequence of the young salmon not showing up in salvage (Figure 2). For me, the high risk factors are clear.

  1. The lack of salvage simply indicates that few of the migrating salmon survive upon entering the Delta under high exports. High late-November and early-December south Delta exports are a high risk to the juvenile winter-run survival. Traditional high December exports of up to 65% of Delta inflow allowed under D1641 water quality standards are a major risk factor for winter-run salmon that must be changed.
  2. Declining flows below Keswick Dam (rivermile 300) during the fall, combined with the lack of flow pulses, are also a real concern. Juvenile salmon that pass Red Bluff (river mile 240) in September and October are sustained in low flow conditions for nearly 200 miles of modified river channel until the first rains in late November or early December. And the spawning reach directly downstream of Keswick gets no added flow even when it rains, because inflows to Shasta Reservoir are all captured.

For additional information, see agency discussions and data presentations in: http://www.westcoast.fisheries.noaa.gov/publications/Central_Valley/Water%20Operations/Delta%20Operations%20for%20Salmonids%20and%20Sturgeon/DOSS%20WY%202018/winter-run_juvenile_production_estimate__jpe__for_brood_year_2017_-_january_29__2018__1_.pdf

Figure 1. Juvenile winter-run salmon estimated passage and stream flow at Red Bluff (rivermile 240) from late summer 2017 to June 2018.

Figure 2. Lower Sacramento River screw trap collections at Knights Landing (rm 90) since August 2017 along with flow, turbidity, and water temperature. Note late November catch event during flow pulse.

Figure 3. South Delta exports in fall 2017. Note peak exports mid-November through early December – total 10,000-11,000 cfs (22,000 acre-ft per day). Chinook salvage is shown as zero.

Figure 4. Flow through Delta Cross Channel August through December 2017. Note sporadic opening late September through November 2017, and closure at end of November.

Figure 5. Delta outflow August through December 2017.

Figure 6. Salinity (EC) near Rio Vista on lower Sacramento River channel in the Delta, August through December 2017.

Figure 7. Salinity (EC) near Jersey Pt on lower San Joaquin River channel in the Delta, August through December 2017.

Figure 8. Juvenile winter-run salmon estimated passage and stream flow at Red Bluff (rm 240) from late summer 2017 to June 2018.

Figure 9. Juvenile winter-run salmon estimated passage at Knights Landing (rivermile 90) and stream flow at Wilkins Slough (rivermile 125) from late summer to fall 2018. Note early December pulse of fish, flow, and turbidity.

Figure 10. Export rates from two south Delta pumping plants (Tracy TRP and Banks HRO) summer and fall 2018.

Figure 11. Lower Sacramento River flow at Freeport (FPT, rm 55) and Delta outflow (DTO) summer and fall 2018.