Crustaceans and large rotifers were collected from three Northeastern U.S. lakes, Lake Awosting (fishless), Lake Minnewaska (piscivores only), Mohonk Lake (planktivores and piscivores), from 2013-2018 to assess differences in community composition, density, and biomass across lakes with different fish communities. In 2017, we collected zooplankton at four discrete depths within each lake (1m, 5m, 8m, and 12m for Mohonk/15m for Awosting and Minnewaska) on three separate sampling occasions during the summer using a Van Dorn sampler. Zooplankton were filtered with a 125-mm mesh sieve and preserved in 70% EtOH in the field. From 2013-2018, 10m vertical tows were also collected using an 80 um Wisconsin plankton net in each lake. These datasets include abundance of organisms across spatial and temporal scales, as well as the individual size and taxonomic identification for all individuals counted.