Evaluation of a large-scale flow manipulation to the upper San Francisco Estuary: Response of habitat conditions for an endangered native fish

Abstract

While flow is known to be a major driver of estuarine ecosystems, targeted flow manipulations are rare because tidal systems are extremely variable in space and time, and because the necessary infrastructure is rarely available. In summer 2018 we used a unique water control structure in the San Francisco Estuary (SFE) to direct a managed flow pulse into Suisun Marsh, one of the largest contiguous tidal marshes on the west coast of the United States. The action was designed to increase habitat suitability for the endangered Delta Smelt Hypomesus transpacificus, a small osmerid fish endemic to the upper SFE. The approach was to operate the Suisun Marsh Salinity Control Gates (SMSCG) in conjunction with increased Sacramento River tributary inflow to direct an estimated 160 x 10 6 m 3 pulse of low salinity water into Suisun Marsh during August, a critical time period for juvenile Delta Smelt rearing. Three-dimensional modeling showed that directing additional low salinity water into Suisun Marsh ("Flow Action") substantially increased the area of low salinity habitat for Delta Smelt that persisted beyond the period of SMSCG operations. Field monitoring showed that turbidity and chlorophyll were at higher levels in Suisun Marsh, representing better habitat conditions, than the upstream Sacramento River region throughout the study period. The Flow Action had no substantial effects on zooplankton abundance, nor did Suisun Marsh show enhanced levels of these prey species in comparison to the Sacramento River. Fish monitoring data suggested that small numbers of Delta Smelt colonized Suisun Marsh from the Sacramento River during the 2018 Flow Action. Comparison of the salinity effects of the Flow Action to historical catch data for Suisun Marsh further supported our hypothesis that the Flow Action would have some benefit for this rare species. Our study provides insight into both the potential use of targeted flow manipulations to support endangered fishes such as Delta Smelt, and into the general response of estuarine habitat to flow management.

Large‐Scale Flow Management Action Drives Estuarine Ecological Response

“…The results of this study and Sommer et al (2020) indicate that the SMSCG operations and flow pulse altered aquatic habitat in Suisun Marsh. Examining long-term data from fisheries monitoring programs revealed limited impacts on the overall aquatic community structure but FIGURE 6.…”

“…We found that implementation of the SMSCG action and coincident flow pulse resulted in a clear and rapid decline in salinity within the marsh. Results from this study and from Sommer et al (2020) have important management implications due to the role of salinity in shaping aquatic food webs and species assemblages in estuaries (Barletta et al 2005;Bernhard et al 2007). Although the salinity changes were not extreme, earlier research suggested that broad guilds of species in the Bay-Delta respond strongly to shifts in regional salinity (Feyrer et al 2015); hence, the observed changes had the potential to affect broader community patterns.…”

Use of a Managed Flow Pulse as Food Web Support for Estuarine Habitat

“…Examples of targeted flow actions in the San Francisco Estuary include: (1) managed seasonal inundation experiments in Yolo Bypass to support native fish rearing (Katz et al 2017;Sommer et al , 2020b; (2) a summer 2018 effort to direct more low-salinity flow into Suisun Marsh-a key region in the system for many species-using a unique water control structure (Sommer et al 2020a); and (3) the North Delta flow action described in the current study. However, there is a major conceptual difference between the Suisun Marsh (Sommer et al 2020a) and Yolo Bypass (Sommer et al 2008(Sommer et al , 2020b experiments and the current effort. The North Delta flow action represents a rare but increasingly important example of a targeted action in a specific geographic region of the estuary.…”

Monitoring Turbidity in San Francisco Estuary and Sacramento–San Joaquin Delta Using Satellite Remote Sensing

“…Overview. As a test application for this algorithm as an evaluation tool, we used this approach to examine water quality changes during a novel 2018 flow action to support Delta Smelt (California Natural Resources Agency 2016; Sommer et al 2020). CDWR lead a pilot study in collaboration with multiple agencies.…”

“…While CDWR did not expect that the action would change turbidity in any of the regions, we examined spatial and temporal patterns to see if there was evidence of differences following the action. Sommer and colleagues describe outcomes in more detail, observing an overall improvement in habitat quality with a focus on salinity and other biological metrics (Sommer et al 2020). The following sections describe our approach toward examining the variability of turbidity most likely associated with the Gates action while accounting for tidal stage and height.…”