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