Cladoceran zooplankton were collected and identified from spring and summer samples from vegetated and open water areas of 26 remnant glacial lakes in Dickinson County, Iowa. The purpose of the study was to determine the factors influencing the structure and composition of zooplankton assemblages as a tool for aiding environmental management of the region's prairie pothole wetlands and ponds. The ponds were assorted into five categories based on morphometric features and productivity: ‘chain lakes’ defined large, deep, interconnected lakes; ‘algal potholes’ were small pothole wetlands dominated by algal primary producers; ‘weedy potholes’ denoted similar ponds dominated by macrophytic vegetation; ‘sloughs’ were similarly dominated by macrophytes, but found along intermittent waterways subject to drying; and ‘walleye ponds’ were kettle-hole ponds modified for the production of gamefish. Multivariate analyses and similarity indices were used to determine the relationship between cladoceran assemblages and the five major lake types. Each lake type contained a distinct cladoceran assemblage that was influenced by the abundance of macrophytes and probably also by fish, although fish species composition was not directly measured. Cladoceran diversity also increased with increased predominance of macrophytes among lakes, and within the same lake in different seasons and sampling locations. A model was built to describe the relationship between cladoceran assemblages and macrophytes that could be used in management or paleoecological applications. If prairie potholes are to be managed for high invertebrate diversity to support waterfowl, our results promote plans that diversify benthic structure within ponds. Advanced eutrophication and conversion of existing potholes to game fish rearing ponds severely limit the abundance and composition of microcrustaceans, which is likely to alter upper levels of the food web.