Longfin Smelt February 2019

In my last update on the status of longfin smelt (February 2018), I decried the continuing decline of the Bay-Delta population of longfin, which are listed under the California Endangered Species Act.  The fall index for 2018 indicates continued low population levels (Figures 1 and 2), with 10 to 100 times higher production in wetter years than dry years.  After the very poor recruitment in 2015 and 2016, there was some recovery in wetter years 2017 and 2018.  Despite record low spawner numbers in 2015 and 2016, recruits increased with wetter years 2017 and 2018, which in turn could lead to improvement in 2019 and beyond with indices above 100 (log 2.0 in figure 2) or perhaps even near 1000 (log 3.0 in figure 2).  If drought returns, bets are off.

Figure 1. Fall Midwater Trawl Index for longfin smelt, 1967-2018. Source: http://www.dfg.ca.gov/delta/data/fmwt/indices.asp

Figure 2. Longfin Recruits (Fall Midwater Trawl Index) vs Spawners (Index from two years prior) in Log10 scale. The relationship is very strong and highly statistically significant. Adding Delta outflow in winter-spring as a factor makes the relationship even stronger. Recruits per spawner are dramatically lower in drier, lower-outflow years (red years). Data source: http://www.dfg.ca.gov/delta/data/fmwt/indices.asp.

Winter Pulsed Flows for Fall Run Salmon

There has been a series of storms in the Central Valley in early winter 2019 that have stimulated the migration of salmon fry and smolts in the lower Sacramento River toward the Bay-Delta (Figure 1). However, these storms have not created flow pulses in the 25 miles of prime spawning habitat in the Sacramento River directly downstream of Keswick Dam (River Mile 300) (Figures 2 and 3). High flows at Bend Bridge (RM 250) have originated from largely un-dammed Cow, Cottonwood, and Battle creeks. Although inflow to Shasta and Keswick reservoirs has exceeded 50,000 cfs during two recent storm events (Figure 4), these reservoirs are releasing only a few thousand cfs.

Based on the Red Bluff screw trap catch (top chart in Figure 1), there are likely many wild fry in the upper river directly downstream of Keswick Dam that could take advantage of flow pulses to start their 300–mile journey toward the San Francisco Bay-Delta and its optimal fry rearing habitat. Flow pulses of 3000-5000 cfs during storm events added to the existing Keswick release could go a long way toward increasing the production of wild fall-run Chinook salmon.

Figure 1. Screw trap collections of fry fall-run salmon at Red Bluff (RM 240) and Tisdale Weir (RM 120) August 2018 to mid-January 2019.

Figure 2. Sacramento River flow at Keswick Dam (RM 300) (red line) and Bend Bridge (RM 250) (green line) 10/1/18-1/16/19.

Figure 3. Map of upper 100 miles of Sacramento River downstream of Keswick Dam with approximate percent of salmon spawning by sub-reach. (CDFW data)

Figure 4. Inflow to Shasta Reservoir in January 2019.

Suisun Bay Zooplankton in Droughts

Suisun Bay zooplankton are important prey for Bay-Delta fish populations, including smelt and juvenile salmon.  During the recent 2012-2016 drought, the State Water Board issued temporary urgent change orders (TUCOs) that allowed lower Delta outflow than would normally be required in Critically Dry water years.  Specifically, those Board orders allowed lower outflow in spring of 2014 and 2015. To evaluate the effects of these orders, I looked at June outflow versus June density of cladoceran and calanoid copepods, the primary fish prey in Suisun Bay and Marsh, the prime east Bay nursery area.

Zooplankton sampling stations in area of Suisun Bay and Suisun Marsh. I used June survey densities for stations 28, 32, 48, 54, and 60 to represent food available to young salmon and smelt.

Cladocerans

Cladocerans, sometimes called “water fleas,” are generally most prevalent in freshwater portions of the estuary, and would be expected to have lower density as brackish water encroaches in Suisun Bay with lower outflow. Cladoceran density was near zero in June 2014 and 2015, when outflow fell below 5000 cfs under the TUCOs (Figures 1 and 2) and EC reached an unprecedented 13-16 millimhos in June at Mallard Island in Suisun Bay (CDEC data). Cladoceran densities were highly variable in the outflow range of 6000-8000 cfs.

Calanoid Copepods

Calanoid copepods are another important prey of juvenile fish in Suisun Bay/Marsh. They reside in fresh and brackish waters of the Bay-Delta estuary. Calanoid copepod adult density was near zero in June 2014 and 2015, when outflow fell below 5000 cfs under the TUCOs (Figures 3 and 4) and EC reached an unprecedented 13-16 millimhos in June at Mallard Island in Suisun Bay (CDEC data). Calanoid copepod adult densities were highly variable in the outflow range of 6000-8000 cfs.

Conclusion

Maintaining Delta outflow in spring at least as great as is required by existing water quality standards is important in maintaining the productivity of zooplankton in Suisun Bay and Suisun Marsh. June outflows greater than existing requirements generally increased the productivity of these important prey for fish.

Figure 1. Density/m3 (log transformed) of total cladocerans in Suisun Bay/Marsh in June surveys 2000-2017. Note very low densities during 2012-2016 drought, especially in 2014 and 2015 when TUCOs allowed outflow to fall below 5000 cfs.

Figure 2. Density/m3 (log transformed) of total cladocerans in Suisun Bay/Marsh in June surveys 2000-2017 versus average daily June Delta outflow for the year. Note the high variability in density in the outflow range of 6000-8000 cfs. The two dots on the x axis represent 2014 and 2015.

Figure 3. Density/m3 of calanoid copepod adults in Suisun Bay/Marsh in June surveys 2000-2017.
Note very low densities during the 2013-2015 drought, especially in 2014 and 2015 when TUCOs allowed outflow to fall below 5000 cfs.

Figure 4. Density/m3 of calanoid copepod adults in Suisun Bay/Marsh in June surveys 2000-2017 versus average daily June Delta outflow for the year. Note the high variability in density in the outflow range of 6000-8000 cfs. The two dots just above the x axis represent 2014 and 2015.

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

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

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.