Category Archives: Smelt

Hatchery Delta Smelt 2021

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Efforts continue to gain approval for releasing hatchery-raised delta smelt in the San Francisco Bay-Delta Estuary. However, given a poor prognosis for a successful introduction, the chances of approval are not good.1  The biggest obstacle is the absence of a location to release the hatchery-raised fish that will allow their survival and thus contribute to the species’ recovery. Another problem is the potential detrimental effect on the remaining wild smelt from genetic compromise.

To me, the answer to the second issue is clear. With few if any “wild” delta smelt left on Earth, it is essential to get as many hatchery smelt out into the wild as soon as possible to save the species. Let the genetics get worked out later by Mother Nature.

Two locations for release of hatchery smelt seem most plausible: the low salinity zone in the west Delta/eastern Suisun Bay and the Deep-Water Shipping Channel in the north Delta. These are primary late spring and early summer nursery areas that are most likely to have the right habitat conditions (water temperature and low salinity) and food supply. These two locations were the last known concentrations of juvenile delta smelt (Figure 1) from the last strong adult spawn in 2012 (Figure 2).

The better of the two sites is the eastern-Bay/west-Delta location, because the ship-channel gets too warm by summer (Figure 3). In contrast, the region between Collinsville in eastern Suisun Bay and Decker Island in the west Delta is cooler and within the low salinity zone (Figures 4 and 5). A nighttime near-bottom release into cooler, deeper channel waters would give the hatchery smelt at least a minimum opportunity to acclimate to the warm Bay-Delta waters.2

Figure 1. Last known prime late spring and early summer nursery area of delta smelt (2012, 20-mm survey). Red lines denote approximate location of X2 (~2000-4000 EC) at the time.

Figure 2. Adult delta smelt catch index from monthly winter trawl surveys 2002-2021.

Figure 3. Water temperature (ºC) and salinity (EC) in spring 2020 in Deep Water Ship Channel.

Figure 4. Water temperature (C) and salinity (EC) in spring 2021 in Sacramento River channel near Collinsville in eastern Suisun Bay.

Figure 5. Water temperature (ºC) and salinity (EC) in spring 2021 in Sacramento River channel near Decker Island in the western Delta.

Longfin Smelt 2021 – Another Poor Year

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The Bay-Delta longfin smelt population, listed as threatened under the California Endangered Species Act, is having another poor year because of the Bay-Delta habitat conditions in critically dry year 2021. Winter spawning and early rearing habitat conditions were poor due to low Delta outflow. Spring conditions have been similarly poor, with low Delta outflows and high water temperatures. Summer conditions will be even worse.

Winter

As in prior dry years, longfin spawned in the Delta in winter 2021. Their newly hatched pelagic larvae accumulated in the low salinity zone in eastern Suisun Bay close to Chipps Island near the city of Pittsburg (Figures 1 and 2). In wetter years, longfin larvae accumulate further west in western Suisun Bay and San Pablo Bay, and are also more likely to spawn in Bay tributaries, especially the Napa River. With Delta export pumps diverting about one-third of winter freshwater inflow to the Delta and Bay, significant numbers of larval longfin smelt were susceptible to being drawn into the central and south Delta, away from their low salinity zone nursery area in eastern Suisun Bay.

Spring

With low spring Delta outflows of 3000-6000 cfs, similar to critical drought years 2014 and 2015 (Figure 3), longfin juveniles were concentrated in the low salinity zone in the western Delta (Figure 4). In that location, they are more vulnerable to Delta exports than in the prior winter, and are also subjected to warmer water temperatures (Figure 5) detrimental to their survival (Jeffries et al. 2016).1

Summer

The prognosis for the summer is grim, given expected water temperatures over 68ºF under low flows allowed under the Temporary Urgency Change Petition (Figure 5).

Population Response

The combination of low outflow (poor habitat), vulnerability of larval and juvenile longfin smelt to export, and reduced numbers of adult spawners that have survived in recent years leads to low population recruitment (Figure 3).2

Summary and Conclusions

In a critically dry year like 2014, 2015, or 2021, Delta outflows should not fall below 6,000-8,000 cfs on a daily or tidally filtered basis (Figure 3). Such outflows keep the low salinity zone west of the Delta in Suisun Bay, where water would be cooler and longfin would be less likely to be drawn into the central and south Delta. State recovery planning for longfin smelt should also proceed as has been recommended.3

Figure 1. Catch distribution of larval longfin smelt in the mid-January 2021 larval fish survey. Red area is approximate location of low salinity zone. Red arrow is net direction of west Delta flow toward south Delta export pumps. Data Source: CDFW survey online report.

Figure 2. Catch distribution of larval longfin smelt in the February 2021 larval fish survey. Red area is approximate location of low salinity zone. Red arrow is net direction of west Delta flow toward south Delta export pumps. Data Source: CDFW survey online report.

Figure 3. Delta outflow in spring and early summer 2014, 2015, and 2021. Note the sharp decline in late May 2021 (blue line) following approval of Temporary Urgency Change Petition (TUCP).

Figure 4. Catch distribution of larval longfin smelt in the May 2021 20-mm fish survey #5. Red area is approximate location of low salinity zone (2-4 EC). Blue areas are higher salinity zones in Bay. Red line is approximate location of X2. Data Source: CDFW survey online report.

Figure 5. Longfin Recruits (Fall Midwater Trawl Index) vs Spawners (Index from two years prior) in Log10 scale by water year. The relationship is very strong and highly statistically significant. Adding Delta outflow in winter-spring as a factor makes the relationship even stronger. The 2019 brood year index was lower than expected, given the potential number of spawners (from the relatively high 2017 index) and 2019 having been a wet year. The 2020 index is as expected for a dry year, with low spawner numbers.

Longfin Smelt – 2020

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In a February 2020 post on the status of longfin smelt, I lamented the poor 2019 population index (Figure 1) and thus made a grim prediction for the future of the Bay-Delta sub-population of this state-listed endangered species.  The index in wet year 2019 should have been 10 times higher (one higher in log number).  Preliminary survey results suggest that the 2020 population index for longfin smelt will likely be as poor as those in 2018 and 2019.

In Figure 1 below, the 2020 index will likely show as a red 20 just above the red 14.  Most of the 2020 spawners came from the 2018 spawners (green 18 in Figure 1).  Like the 2018 spawn, the 2020 year class grew up in a drier year, upstream in Suisun Bay and the western Delta (Figure 2), as compared to a more western Bay distribution like wet year 2019 (Figure 3).

I am very concerned what will happen if winter 2021 stays dry and there are thus two dry water years in a row (2020 and 2021).  This would drive the 2021 production index down to 2015-16 levels.  Coupled with the absence of Fall-X2 flows in 2020 and the unusually low 2019 longfin index, a second straight dry year presents a serious threat to the population index in 2021 and future years.

Figure 2. Longfin smelt catch distribution in 2020 Survey 1 of 20-mm Survey. Delta outflow was 8,000-20,000 cfs. Source.

Figure 3. Longfin smelt catch distribution in 2019 Survey 1 of 20-mm Survey. Delta outflow was 160,000-180,000 cfs. Source.

 

Delta Smelt – 2020 Status

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In a March 2020 post, I described the status of the Delta smelt through 2019.  This post updates the status with the most recent 2020 information.  Delta smelt continue to be absent from the standard long-term surveys and their related indices.  However, some Delta smelt were collected in 2020 in selected locations of the Bay-Delta during focused intensive special surveys designed to find remaining survivors.  Larval and juvenile Delta smelt were collected in low numbers in the Bay and north Delta (Figure 1).  Pre-adult Delta smelt were also collected in summer trawl surveys (Figure 2).

The north Delta habitats where a few Delta smelt persevere continue to be plagued by constant stressful if not lethal water temperatures (Figures 3 and 4).

As I stated in a prior post, Delta smelt would benefit from increased net flows through the north Delta during the spring and summer.

Figure 1. Numbers of larval and juvenile Delta smelt collected in the spring Enhanced Delta Smelt Monitoring (EDSM) 20-mm nets. Source.

Figure 2. Numbers of pre-adult Delta smelt collected in the summer Enhanced Delta Smelt Monitoring (EDSM) Kodiak trawls. Source.

Figure 3. May through September 2020 water temperature and net tidally-filtered flow in the lower ship channel near Rio Vista. Note water temperatures fall 1-2ºC when net flows increase.

Figure 4. May through September 2020 water temperature and net tidally-filtered flow in Cache Slough near Rio Vista. Note water temperatures generally fall 1-2ºC when net flows increase.

May-September Delta Water Temperature Standard Needed

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In a 9/22/20 post, I suggested summer Delta outflow standards. In this post I suggest a spring-summer water temperature standard for the Delta as further protection for salmon and smelt. Water temperatures above 23oC (73oF) are harmful to salmon and smelt, which live and migrate through the north and west Delta throughout the summer. Much of the Delta smelt population that remains is located in these regions especially in dry years.1 Spring-run and winter-run salmon migrate upstream through the area in late spring. Fall-run salmon migrate upriver through the summer.

Harm occurs as stress, higher predation, avoidance reactions, poor growth, and reduced long-term survival and reproduction. At higher temperatures (>23oC) migration blockage and mortality occurs. Such temperatures are commonly reached or exceeded in the north Delta even in wetter, water-abundant years.

High water temperatures occur in the Delta when there are high air temperatures and/or low freshwater inflow and outflow. Such conditions are becoming more frequent with climate change. A good example occurred in water year 2020, which featured low precipitation, low snowpack, and high air temperatures.2 Because water managers cannot control air temperatures or watershed precipitation, they must manage Delta inflows from reservoir releases and outflows through the Delta to improve water temperature control in May-September, especially in drier years.

To protect smelt and salmon, there need to be reasonable water temperature standards in the Delta. The existing water temperature standard in the lower Sacramento River above the Delta is 68oF, but managers of the state and federal water projects pay it almost no heed. There is no existing standard for the Delta. The north Delta water quality standard for the Sacramento channel in wet years should be 70oF (21oC) at Freeport and at Rio Vista. In normal and dry water years, the standard should be 72oF (22oC) at Freeport and at Rio Vista. In critical drought years, the State Water Board needs to require additional Delta inflow and curtail exports as needed to respond to extreme events (e.g., water temperatures greater than 75oF during heat waves). At critical times, a change of only a degree or two will help limit fish stress and mortality.

Higher Delta outflow and lower exports are appropriate prescriptions for maintaining reasonable water temperatures in the Delta (see Figures 1-3 and caption notes). For example, in July and August 2020 (Figures 1-3), increased inflow into the 14,000-16,000 cfs range from 12,000 cfs at Freeport could have held water temperature below 22oC. Note in Figure 3 that increased inflow can be captured by south Delta exports (Figure 3). However, during heat waves under extreme drought conditions, the State Board should also limit exports to retain outflows from the Delta to keep the low salinity zone out of the warmer Delta. Otherwise, exports will reduce the portion of Delta inflows (Freeport flows) that reach Rio Vista.

Such standards are achievable, albeit at significant water supply cost. They are worth the effort. High summer water temperatures, such as those that occurred in wet year 2019 and dry year 2020, must be mitigated. The 23-25oC conditions in summer 2020 (portrayed in Figures 1-3) should not occur, and would not under the suggested Delta water temperature standard. For wet years such as 2019 (Figure 4) and 2017 (Figure 5), water temperatures should be kept at or below 70oF (21oC) by maintaining Freeport near 20,000 cfs as needed.

In summary, Delta water quality standards should be adopted for inflow, outflow, and water temperature to protect salmon and smelt in the warmer months of the year, May-September. Such standards are needed because of recent changes in water project operations and the effects of climate change.

Figure 1. Water temperature and salinity in the west Delta near Rio Vista in spring-summer 2020. Note Delta draining in neap-tide periods generally brings warmer water downstream into the west Delta, except in mid-August event when a heat wave drove water temperatures up into 23-25oC range. This event was accentuated by higher exports and associated high Delta inflows.3

Figure 2. Water temperature and net river flow (tidally filtered) in the lower Sacramento River at Freeport in the north Delta in spring-summer of dry year 2020. Note that it took flows at or greater than 16,000 cfs to keep temperatures near 70oF (21oC).

Figure 3. Sacramento River flow at Freeport (FPT), water temperature at Rio Vista (RVB), and south Delta exports at Tracy (TRP) and Banks (HRO) pumping plants in south Delta from May-Oct 2020.

Figure 4. Water temperature and net river flow (tidally filtered) in the lower Sacramento River at Freeport in the north Delta in spring-summer of wet year 2019. Note that it took flows at or greater than 16,000 cfs to keep temperatures near 70oF (21oC).

Figure 5. Sacramento River flow at Freeport (FPT-Y1) and water temperature at Freeport (FPT-Y2) and Rio Vista (RVB-Y2) from May-Oct 2017.