© 2020 by the authors. Licensee MDPI, Basel, Switzerland. The diversity of species on a landscape is a function of the relative contribution of diversity at local sites and species turnover between sites. Diversity partitioning refers to the relative contributions of alpha (local) and beta (species turnover) diversity to gamma (regional/landscape) diversity and can be influenced by the relationship between dispersal capability as well as spatial and local environmental variables. Ecological theory predicts that variation in the distribution of organisms that are strong dispersers will be less influenced by spatial properties such as topography and connectivity of a region and more associated with the local environment. In contrast, the distribution of organisms with limited dispersal capabilities is often dictated by their limited dispersal capabilities. Small and ephemeral wetlands are centers of biodiversity in forested ecosystems. We sampled 41 small and ephemeral wetlands in forested ecosystems six times over a two-year period to determine if three different taxonomic groups differ in patterns of biodiversity on the landscape and/or demonstrate contrasting relationships with local environmental and spatial variables. We focused on aquatic macroinvertebrates (aerial active dispersers consisting predominantly of the class Insecta), amphibians (terrestrial active dispersers), and zooplankton (passive dispersers). We hypothesized that increasing active dispersal capabilities would lead to decreased beta diversity and more influence of local environmental variables on community structure with less influence of spatial variables. Our results revealed that amphibians had very high beta diversity and low alpha diversity when compared to the other two groups. Additionally, aquatic macroinvertebrate community variation was best explained by local environmental variables, whereas amphibian community variation was best explained by spatial variables. Zooplankton did not display any significant relationships to the spatial or local environmental variables that we measured. Our results suggest that amphibians may be particularly vulnerable to losses of wetland habitat in forested ecosystems as they have high beta diversity. Consequently, the loss of individual small wetlands potentially results in local extirpations of amphibian species in forested ecosystems.