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Effects of tidally varying river flow on entrainment of juvenile salmon into Sutter and Steamboat Sloughs

June 15, 2021

Survival of juvenile salmonids in the Sacramento–San Joaquin Delta (Delta) varies by migration route, and thus the proportion of fish that use each route affects overall survival through the Delta. Understanding factors that drive routing at channel junctions along the Sacramento River is therefore critical to devising management strategies that maximize survival. Here, we examine entrainment of acoustically tagged juvenile Chinook Salmon into Sutter and Steamboat sloughs from the Sacramento River. Because these sloughs divert fish away from the downstream entrances of the Delta Cross Channel and Georgiana Slough (where fish access the low-survival region of the interior Delta), management actions to increase fish entrainment into Sutter and Steamboat sloughs are being investigated to increase through-Delta survival. Previous studies suggest that fish generally “go with the flow”—as net flow into a divergence increases, the proportion of fish that enter that divergence correspondingly increases. However, complex tidal hydrodynamics at sub-daily time-scales may be decoupled from net flow. Therefore, we modeled routing of acoustic tagged juvenile salmon as a function of tidally varying hydrodynamic data, which was collected using temporary gaging stations deployed between March and May of 2014. Our results indicate that discharge, the proportion of flow that entered the slough, and the rate of change of flow were good predictors of an individual’s probability of being entrained. In addition, interactions between discharge and the proportion of flow revealed a non-linear relationship between flow and entrainment probability. We found that the highest proportions of fish are likely to be entrained into Steamboat Slough and Sutter Slough on the ascending and descending limbs of the tidal cycle, when flow changes from positive to negative. Our findings characterize how patterns of entrainment vary with tidal flow fluctuations, providing information critical for understanding the potential effect of management actions (e.g., fish guidance structures) to modify routing probabilities at this location.

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1Sponsored by the Delta Science Program and the UC Davis Muir InstituteABSTRACTSurvival of juvenile salmonids in the Sacramento–San Joaquin Delta (Delta) varies by migration route, and thus the proportion of fish that use each route affects overall survival through the Delta. Understanding factors that drive routing at channel junctions along the Sacramento River is therefore critical to devising management strategies that maximize survival. Here, we examine entrainment of acoustically tagged juvenile Chinook Salmon into Sutter and Steamboat sloughs from the Sacramento River. Because these sloughs divert fish away from the downstream entrances of the Delta Cross Channel and Georgiana Slough (where fish access SFEWS Volume 19 | Issue 2 | Article 4https://doi.org/10.15447/sfews.2021v19iss2art4* Corresponding author: rperry@usgs.gov1 Western Fisheries Research Center US Geological Survey Cook, WA 98605 USA2 California Water Science Center US Geological Survey Sacramento, CA 95819 USA3 Current address: Mid-Columbia Fish and Wildlife Conservation Office Yakima Basin Program US Fish and Wildlife Service Yakima, WA 98903 USAthe low-survival region of the interior Delta), management actions to increase fish entrainment into Sutter and Steamboat sloughs are being investigated to increase through-Delta survival. Previous studies suggest that fish generally “go with the flow”—as net flow into a divergence increases, the proportion of fish that enter that divergence correspondingly increases. However, complex tidal hydrodynamics at sub-daily time-scales may be decoupled from net flow. Therefore, we modeled routing of acoustic tagged juvenile salmon as a function of tidally varying hydrodynamic data, which was collected using temporary gaging stations deployed between March and May of 2014. Our results indicate that discharge, the proportion of flow that entered the slough, and the rate of change of flow were good predictors of an individual’s probability of being entrained. In addition, interactions between discharge and the proportion of flow revealed a non-linear relationship between flow and entrainment probability. We found that the highest proportions of fish are likely to be entrained into Steamboat Slough and Sutter Slough on the ascending and descending limbs of the tidal cycle, when flow changes from positive to negative. Our findings characterize how patterns of entrainment vary with tidal flow fluctuations, providing information critical for understanding the potential effect of management RESEARCHEffects of Tidally Varying River Flow on Entrainment of Juvenile Salmon into Sutter and Steamboat Sloughs Jason G. Romine1,3, Russell W. Perry*1, Paul R. Stumpner2, Aaron R. Blake2, Jon R. Burau2
2VOLUME 19, ISSUE 2, ARTICLE 4actions (e.g., fish guidance structures) to modify routing probabilities at this location. KEY WORDSTelemetry, juvenile salmon, migration routing, survivalINTRODUCTIONThe Sacramento–San Joaquin River Delta (hereafter referred to as “the Delta”) is a complex series of channels and embayments in west central California of the United States. The Delta has undergone drastic transformation through construction of dikes, levees, reclaimed land, dredged canals and cuts, and water export projects (Nichols et al. 1986). The loss of habitat coupled with introduction of non-native piscivorous fishes has led to the decline of several salmonid stocks that utilize the Delta (Lindley 2009; National Marine Fisheries Service 2014). The physical complexity of the Delta poses significant challenges for understanding how juvenile salmon negotiate the complex channel network and survive in different migration routes. Yet such information is critical for understanding how water-management actions, such as operation of water diversions, influence survival of juvenile salmon.Through-Delta survival of juvenile Chinook Salmon that emigrate from the Sacramento River ranges from 10% to 80%, depending on river flow and migration route (Perry et al. 2018). The Delta can be broken down into four primary routes: (1) Sacramento River, (2) Steamboat and Sutter sloughs, (3) Georgiana Slough, and (4) Delta Cross Channel (DCC). Fish that remain in the Sacramento River consistently have the highest survival (Perry et al. 2010, 2013, 2018). However, fish that enter the interior Delta—the region to the south of the Sacramento River (Figure 1)—have the lowest survival among all routes and survive at less than half the rate of fish in the Sacramento River, likely as a result of longer migration times and exposure to non-native predators (Newman and Brandes 2010; Perry et al. 2018). On average, fish that migrate through Steamboat and Sutter sloughs exhibit survival similar to fish that remain in the Sacramento River at high flows but have lower survival at low flows (Perry et al. 2018). Because of differences in survival among migration routes, the proportion of fish that use each route affects the total survival of the population. Therefore, understanding the drivers behind fish routing in the Delta is imperative to inform management actions that help in the recovery of imperiled salmonid populations in the Central Valley. For example, Perry et al. (2013) found that total survival through the Delta could be increased by up to 7 percentage points by eliminating entrainment into Georgiana Slough and the DCC. These findings led to investigation of management actions to reduce entrainment into the DCC (Plumb et al. 2016) and Georgiana Slough (Perry et al. 2014). Both physical and non-physical barriers have been tested at the entrance to Georgiana Slough divergence (Perry et al. 2014; Romine et al. 2016). A non-physical barrier was able to reduce entrainment to the interior Delta through Georgiana Slough (Perry et al. 2014), but a floating fish-guidance structure reduced entrainment to a lesser extent (Romine et al. 2016). Research and engineering solutions to minimize entrainment have focused on the Georgiana Slough divergence, the DCC divergence, and the Old River divergence in the San Joaquin River (Buchanan et al. 2013; SJRG 2013). However, there has been little focus on understanding fish routing dynamics at other primary river junctions in the Delta, such as Sutter and Steamboat sloughs. Sutter and Steamboat sloughs diverge from the Sacramento about 10 km upstream from the DCC and Georgiana slough, and represent the first major junction that juvenile salmon encounter as they enter the Delta from the Sacramento River (Figure 1). Because Sutter and Steamboat sloughs are upstream of the entrance to the interior Delta via the DCC and Georgiana Slough (Figure 1), juvenile salmon that enter Sutter and Steamboat sloughs avoid entrainment into the interior Delta where survival is low. Thus, management actions to increase entrainment could increase overall.