This data release includes zooplankton data collected from a collaborative effort for Environmental Protection Agency’s Cooperative Science and Monitoring Initiative (CSMI). Zooplankton surveys were conducted during the growing season, from late April to early November, in two Lake Michigan transects in 2010, two Lake Huron transects in 2012, eight Lake Michigan transects in 2015, and nine Lake Huron transects in 2017. Zooplankton samples were collected by whole water-column tows at two or three stations in different bottom-depth categories (i.e., shallow, middle, and deep) in each of the transects. Due to the difference in bathymetry, some transects did not have a deep station. The shallow and middle stations have bottom depths of 11-27 m and 40-51 m, respectively, in both Lakes Michigan and Huron. As Lake Michigan is generally deeper than Lake Huron, the deep stations have bottom depths of 85-112 m in Lake Michigan and 64-90 m in Lake Huron. The dataset includes tables for sampling operation, zooplankton count, and zooplankton individual size, which may be used to derive zooplankton count or biomass per volume.