Wetlands are ecologically valuable and complex systems that both link and buffer aquatic and terrestrial systems. Spatial aspects and metacommunity concepts help explain community structure and dynamics, but metacommunity dynamics have not been applied to multiple interacting classes of organisms in temperate wetlands. The aim of this study was to 1) quantify significant patterns of wetland community structure within a large wetland in Central New York, USA at a variety of scales and on several trophic levels in relation to key elements of the physical and biological environment, and 2) evaluate four paradigms of metacommunity dynamics that may explain that community structure. Data on assemblages of three major interacting community components, having different dispersal abilities (birds, fish, and invertebrates), and environmental conditions were collected from aquatic habitats of different size and connectivity. Analysis of diversity and composition in relation to a size-connectivity index (SCI) showed clear evidence of spatial or environmental influences, or both for all major taxa. Aquatic organisms formed distinct assemblages whose spatial arrangement and associated environmental conditions were consistent with one of the two spatially explicit metacommunity paradigms, Mass Effect, Species Sorting, or both. The study wetland was a relatively productive, metacommunity, populated by members of a post-glacial species pool, and maintained within three major habitat types, large pools connected to small ditch-like habitats, and isolated pools. Metacommunity dynamics differed by organism class, but habitat was clearly heterogeneous, eliminating Patch Dynamics and Neutral Models. Aerial insects showed little metacommunity dynamics, with a weak habitat condition link to the Species Sorting mechanism. Aquatic invertebrates and aquatic vertebrates showed evidence of both Mass Effect and Species Sorting, with strong environment influences emphasizing the latter; social behavior modified Species Sorting for aquatic birds. The multi-taxon approach revealed important couplings among wetland community components; active management of wetland habitat via altered water supply and connectivity may allow aquatic organisms to escape disturbance and recolonize habitat, but will likely change community structure. Controlled experiments on organism demographics and movements would help clarify the processes of community maintenance in this and other wetlands.