Simplification of communities is a common consequence of anthropogenic modification. However, the prevalence and mechanisms of biotic homogenization among wetland systems require further examination. Biota of wetlands in the North American Prairie Pothole Region are adapted to high spatial and temporal variability in ponded-water duration and salinity. Recent climate change, however, has resulted in decreased hydrologic variability. Land-use changes have exacerbated this loss of variability. We used aquatic-macroinvertebrate data from 16 prairie-pothole wetlands sampled between 1992 and 2015 to explore homogenization of wetland communities. Macroinvertebrate communities of small wetlands that continued to cycle between wet and dry phases experienced greater turnover and supported unique taxa compared to larger wetlands that shifted towards less dynamic permanently ponded, lake-like regimes. Temporal turnover in beta-diversity was lowest in these permanently ponded wetlands. Additionally, wetlands that shifted to permanently ponded regimes also experienced a shift from palustrine to lacustrine communities. While increased pond permanence can increase species and overall beta-diversity in local areas previously lacking lake communities, homogenization of wetland communities at a larger, landscape scale can result in an overall loss of biodiversity as the diverse communities of many wetland systems become increasingly similar to those of lakes.