Code and data for Mitchell et al.

Zooplankton are vital primary consumers in aquatic systems, including freshwater reservoirs, yet research is lacking on how reservoir type may affect zooplankton abundance, diversity, and composition. To address this knowledge gap, we undertook a field study of four Columbia River Basin (CRB) reservoirs, including two run-of-river reservoirs (Bonneville and The Dalles) and two storage reservoirs (Cougar and Detroit). Triplicate zooplankton tows and environmental data were collected at each site bimonthly over two years (November 2022-September 2024). We applied PERMANOVA, non-metric multidimensional scaling (NMDS) ordination, hierarchical clustering analysis, indicator species analysis, and ENVFIT to assess zooplankton assemblage patterns and their environmental associations. Run-of-river reservoirs exhibited higher zooplankton diversity (species richness), seasonal variability, and presence of fast-maturing taxa (namely rotifers), while storage reservoirs exhibited lower diversity (species richness) and a greater abundance of copepods. Zooplankton assemblage structure was significantly associated with nitrate and nitrite concentrations and conductivity (higher in run-of-river reservoirs), as well as phosphate levels, Secchi depth, and residence time (higher in storage reservoirs). This study is the first to directly compare differences in zooplankton abundance, diversity, and composition between multiple run-of-river versus storage reservoirs and provides novel insights into how different dam types may influence freshwater food webs and ecosystem dynamics.