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Body size is an important functional trait that can be indicative of ecosystem structure and constraints on growth. Both increasing temperatures and eutrophication of lakes have been associated with a shift toward smaller zooplankton taxa. This is important in the context of climate change, as most aquatic habitats are expected to warm over the coming decades. Our study uses data from over 1000 lakes surveyed across a range of latitudes (26–49°N) and surface temperatures (10–35°C) in the USA during the spring/summer of 2012 to characterize pelagic cladoceran body size distributions. We used univariate and multiple regression modeling to determine which environmental parameters were strongly correlated to cladoceran body size. A strong positive correlation was observed between cladoceran body size and latitude, while a strong negative correlation was observed between cladoceran body size and water temperature. The ratio of zooplankton to phytoplankton, as well as relative total biomass contributions by cladocerans, decreased as trophic state increased. Multiple regression identified temperature-related variables and water clarity as significantly affecting cladoceran body size. These observations demonstrate the dual threat of climate change and eutrophication on lake ecosystems and highlight potential changes in biogeographical patterns of zooplankton as lakes warm.