Estuarine floodplain wetland pools occur adjacent to marine coasts and estuaries throughout the world. In Australia’s dry tropics and sub-tropics, low and irregular rainfall means estuarine wetland pools are isolated for much of the time, resulting in varied within-pool conditions, with chemistry ranging from fresh to hypersaline, depending on the balance between freshwater and marine inputs and the time between connections. Varied physical conditions and irregular connectivity provide the potential for substantial faunal difference among pools. The present study compares the compositions and structures of the fish fauna of a broad cross section of estuarine wetland pools adjacent to the estuary of the Fitzroy River, one of the largest rivers in Australia’s dry tropical/subtropical zone. Ten pools were sampled between February 2004 and May 2005. The total species richness was low, with the 6123 fish recorded over the study, comprising only 44 species. This low species richness was reflected at the individual pool level, with a maximum total richness of 25 species in a single pool. Different pools had faunas that differed as a function of the proportion of the community comprised of marine spawned, compared with freshwater spawned, species. This was a reflection of the extent of connectivity to freshwater and marine systems, which determined both the physical nature of pools and the sources of faunal supply. Despite faunal differences among pools, at a functional level pool fish faunas were dominated by detritivores, regardless of pool type, size, season or connectedness.