ESTUARY PEARLS: Delta smelt monitoring, new research on salmon survival and flow volume

This month, Pearls digs into some nuances of Delta smelt monitoring—and how we can get more bang from our sampling buck—in three related articles from San Francisco Estuary and Watershed Science. Plus, new research on salmon survival and flow volume.

The robust monitoring programs established to track now-rare Delta smelt could benefit other native fishes, too.

Decades ago, resource managers first learned of declining Delta smelt numbers not through surveys targeting the once-abundant native fish, but rather as a byproduct of long-term monitoring programs for non-native striped bass. Now, the authors of a new study published in the March 2021 issue of San Francisco Estuary and Watershed Science advocate for the use of bycatch data from the recently established Enhanced Delta Smelt Monitoring (EDSM) program to better understand juvenile Chinook salmon distribution.
The scope of [this multi-million dollar Delta smelt survey] has not really been seen before in the Estuary,” says lead author Brian Mahardja, a biologist with the US Bureau of Reclamation, “that’s why there was a call to see what else we can gain out of this program.”
The study team, also representing the US Fish and Wildlife Service and the California Department of Water Resources, analyzed juvenile Chinook salmon bycatch data collected through the EDSM to assess its potential to augment data obtained through other fish surveys. They found that some under-sampled regions of the Delta see improved coverage through EDSM, and that the program’s boat-based, labor-intensive random sampling technique “can provide more statistically robust abundance estimates relative to traditional methods.” That said, the authors also concluded that the use of fixed sampling stations and low-tech methods like beach seining, in which a net is operated manually from shore, still provide a cost-effective way to monitor salmon occurrence in certain parts of the Estuary.
The take-home point is about the trade-offs of different sampling methods,” Mahardja said. “It costs a lot to run these programs, and we want to make sure that we’re getting as much as we can out of them.”

Author:Nate Seltenrich | Above: EDSM crew retrieving a net during trawling in Montezuma. Photo by Kate Erly.

Water turbidity in the Sacramento-San Joaquin Delta can be used as a reliable indicator of smelt entrainment rates in the fish screens of the export pumps at the southern edge of the Estuary.

In a new study published in the March 2021 issue of San Francisco Estuary and Watershed Science, researchers Lenny Grimaldo, William Smith, and Matthew Nobriga used advanced statistical approaches to understand what factors best predict Delta smelt entrainment at the pumps. The paper builds upon research that Grimaldo conducted in the 2000s, which provided the basis for regulations established in the 2008 Delta smelt Biological Opinion.
This study reinforces previous work that adult Delta smelt salvage is largely explained by hydrodynamics, water clarity (turbidity), precipitation, and sub-adult abundance,” the authors write.
Historically, when large numbers of smelt began to appear in the salvage screens of the Delta pumps, pumping would be curtailed. Today, Grimaldo says, the fish are so rare that it is almost impossible to rely on salvaged fish as indicators of total entrainment losses.
But we found that turbidity can be used as an important factor to help manage real-time entrainment losses,” he says.
The theory behind this, he explains, is that when the water becomes turbid, the fish—which prefer murky water to clear—migrate upstream and into the pumps. The new findings will help resource agencies better manage Delta exports to help protect the rapidly vanishing species.

Author: Alistair Bland |Above: During the 2015 drought DWR scientists tracked the distribution of turbid water in the Delta to protect endangered fish and water supply. Photo: Florence Low, DWR

New insights into Delta smelt swimming behavior could help locate the increasingly elusive fish and prevent losses at the pumps.

Scientists know that smelt use tidal ebbs and flows to migrate landward to spawn, but the degree to which external cues influence behavior remains unclear. In a new study published in the March 2021 issue of San Francisco Estuary and Watershed Science, researchers used computer modeling to predict smelt distribution based on hypothesized swimming behaviors. Six increasingly complex behaviors were tested. For example, the “passive” category assumes that smelt do not swim at all, simply drifting with currents and tides.
At the other end of the spectrum, the smelt respond to both turbidity and salinity cues. After assigning a behavior to simulated smelt distributed across the Delta, researchers ran a 133-day simulation of water year 2002, then compared the modeled movements with observations from the 2002 Spring Kodiak Trawl Survey. The movement models that most closely matched distributions indicated by the survey data were those that incorporated some form of salinity response triggering migration (either overall salinity in the surrounding water or the rate of salinity increase).  The study acknowledges that further refinements are needed to assess the influence of turbidity on smelt movement, due to the challenge of accurately predicting what is essentially a localized, constantly changing effect.
In addition to providing insight into how Delta smelt respond to environmental cues, the study’s findings could also be used to anticipate the risk of fish being caught in water project facilities. According to Ed Gross, an author of the study, “Delta smelt behavior is likely an intermittent tidal migration, because passive behavior would not accomplish landward migration and persistent tidal migration also results in unrealistic distribution.”
If turbidity and modeling refinements are made, and one or more behavior models match survey observations from multiple water years, the modeling approach developed by the study could provide real-time entrainment risk analysis based on water conditions in the Delta.

Author: Michael Hunter Adamson | Above:Simulated smelt distribution (green dots) representing responses to salinity and turbidity. The area outlined in red is the region of simulated release (black outlined areas are different study regions). Image: Gross, et al.

Electrofishing is a powerful but underutilized tool for monitoring Delta fish, particularly species favoring “structured” habitats that are difficult to sample using more common methods like trawls and seines.

By analyzing fish catch data from past surveys, researchers Ryan McKenzie, of the US Fish and Wildlife Service, and Brian Mahardja, of the US Bureau of Reclamation, determined that electrofishing resulted in better detection rates for many native and non-native species than net-based surveys. Although electrofishing is currently restricted to freshwater areas of the Estuary and is more selective of larger fish and those with swim bladders, McKenzie and Mahardja recommend that resource managers employ the technique more widely to support long-term conservation planning.
Electrofishing, or e-fishing as it’s sometimes known, uses a generator aboard a small boat to pass electricity through the water beneath and in front of the boat.
When the electricity moves through the water, it can immobilize the fish within the zone of being shocked,” says McKenzie. “It’s a really cool method. You’re looking down at the water, and then all of a sudden fish pop out of the water.”
Briefly incapacitated, fish are collected via dip net and placed into a holding tank, where they come to their senses within a minute or so and can be identified, measured, and otherwise studied before being returned to the water. Electrofishing has been used intermittently by various agencies for fish monitoring in the Delta since the early 1980s, but received criticism in the 2000s due to concerns over high injury rates to some species, particularly salmonids.
Since that time, there’s been newer research conducted using more standardized methods for e-fishing, and those are the methods we currently use, which have lower injury rates for those species,” McKenzie says. “That’s why going forward, I think e-fishing is a viable option.”
The study appears in the March 2021 issue of San Francisco Estuary and Watershed Science.

Author: Nate Seltenrich | Photo: Electrofishing in the Delta, courtesy Ryan McKenzie

New research indicates that survival of juvenile Chinook salmon in the Sacramento River system can be significantly boosted by achieving key thresholds for river flow.

The findings, published in the journal Ecosphere, add important context to the general scientific understanding that more water in the river improves fish survival. Previous studies, the authors explain in their paper, have demonstrated that more juvenile salmon migrating toward the sea complete their journey when the Sacramento River system contains more water. Just how much water has been the source of much controversy among user groups.
These studies have not explored the potential nonlinearities between flow and survival, giving resource managers the difficult task of designing flows intended to help salmon without clear guidance on flow targets,” write the authors, led by Cyril Michel of the Institute of Marine Sciences at UC Santa Cruz.
Studying migrating Chinook salmon smolts under a wide range of hydrologic conditions, they found that fewer than three percent of fish carrying acoustic tags were detected after release at flows weaker than about 4,260 cubic feet per second. However, survival jumped to 19 percent at flows ranging between 4,260 and 10,700 cfs; they jumped again to more than 50 percent when the river was carrying between 10,700 and 22,870 cfs. However, fish survival did not improve at even greater flows.
It looks like survival plateaus beyond a certain point,” Michel says. “You can get a lot more bang for your buck if you aim for these thresholds.”
Notably, the researchers calculated that achieving these key flow rates could be possible in most years without adding any extra water to the system by holding reservoir water back at times to release in pulses during heavy migration periods. However, Michel and his team did conclude that just a little extra water—about 150,000 acre-feet per year dedicated to the river system—would be helpful. Michel says he hopes his research will provide a productive guideline for agencies that manage reservoir releases and Delta pumping.

Author: Alistair Bland | Above: Preparing to tag a juvenile salmon. Photo: Cyril Michel

In case you missed it: Talks, plenaries, special sessions, and on-demand videos from the virtual 11th Biennial Bay-Delta Science Conference (BDSC) are now online. The recordings will be available on the BDSC website through the summer.

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