Data are for zooplankton communities sampled in 2016 at the Sheboygan River Area of Concern and two comparison sites, the Kewaunee River and the Manitowoc River, which have similar physical and chemical characteristics. Zooplankton were collected by using tows from depth to the surface with a 63 micrometer mesh plankton net. Physical and chemical data that were sampled concurrently (specific conductance, temperature, pH, and dissolved oxygen) in water by use of a multi-parameter water-quality sonde, and the results of field quality assurance quality control are also included.