San Francisco Estuary and Watershed Science

In 2023 we placed Delta Smelt (Hypomesus transpacificus) into field enclosures for 6 weeks to assess whether an enclosure study could effectively detect Delta Smelt responses to habitat differences during the summer–fall period. Prior enclosure studies have noted high biofouling accumulation during warm months, so we simultaneously tested two biofouling mitigation techniques (cleaning vs. replacement) to better understand their efficacy and potential effects on the fish inside. Fish were held at two sites in the San Francisco Estuary: the Sacramento River near Rio Vista, and Montezuma Slough near Belden’s Landing. Both biofouling mitigation measures were employed at each site. We evaluated water quality and zooplankton inside and outside of the enclosures as well as algal and macroinvertebrate accumulation on the enclosures, and assessed fish survival, health, and diets. We observed significantly improved fish health metrics at Rio Vista compared to Belden’s Landing, potentially associated with higher-quality food, lower water temperatures, and lower water velocities; however, it is unclear whether these differences were in response to the geographic location or to localized enclosure effects, because the fish were unable to seek refuge or forage. We also observed differences in enclosure biofouling and associated macroinvertebrates between the two mitigation measures and saw higher mortality in replaced enclosures but no differences in fish health among survivors. Macroinvertebrates were detected on nearly all enclosures and often made a sizeable proportion of smelt diet biomass, regardless of location or mitigation method, indicating that the enclosures may provide an altered food environment. This study demonstrates the complexity of implementing and interpreting Delta Smelt enclosure studies, and highlights limitations of this tool. Our data offers physiological clues that enhance our understanding of the response of cultured Delta Smelt to differing habitats, but uncertainties highlight that enclosures studies should not be used in isolation to address large-scale management questions.