Northern regions are expected to experience large environmental change over the next few decades. The response of biota will depend on changes in the local environment, regional processes that influence lake connectivity, and species interactions. In 2008, we surveyed 92 lakes and ponds across Wapusk National Park, located on the southwestern shore of Hudson Bay. At each site we assessed water chemistry and zooplankton community composition. In an effort to understand how the aquatic ecosystems will respond to future environmental change, we determined local characteristics (e.g., water chemistry), regional spatial factors (e.g., dispersal), and biotic interactions (e.g., species associations) influencing community composition. Important environmental variables included lake area, pH, ionic composition, total phosphorus, and chlorophyll a; however, spatial variables explained more variation than environmental variables, suggesting that dispersal is an important driver of zooplankton composition in this region. Additionally, species exhibited negative co-occurrence patterns, suggesting biotic interactions are important in structuring the zooplankton communities. As environmental conditions change and the distribution of habitat (i.e., coastal fen, interior peatland, and spruce forest) shifts, evidence that the park's zooplankton community is spatially structured coupled with our suspicion that zooplankton are likely to experience high dispersal levels in Wapusk leads us to suggest zooplankton may indeed be able to track changing environmental conditions within the park, although it remains unclear how species interactions will modify this expectation.