We present data on the spatial distribution of Australian snubfin and humpback dolphins using boat-based line transect surveys in three adjacent bays located in the Far Northern Section of the Great Barrier Reef Marine Park, northeast Queensland. We used Geographic Information Systems (GIS), and both randomization and Mantel tests to examine the relationship between the spatial distribution of the dolphins and three simple, readily quantified, environmental variables: distance to land, distance to river mouth, and water depth. Mantel tests allowed us to make clear inferences about the correlation of the species’ distributions with environmental variables, while taking into account spatial autocorrelation and intercorrelation among variables. Randomization tests indicated snubfin and humpback dolphins occur closer to land than would be expected at random. Two-sample randomization tests indicated snubfin dolphins were found closer to river mouths than were humpback dolphins. Taking spatial autocorrelation into account, Mantel tests indicated all environmental variables were correlated with the spatial distribution of snubfin and humpback dolphins. Interspecific differences in spatial distribution appeared to be related to proximity to river mouths. Preference by snubfin and humpback dolphins for nearshore, estuarine waters is likely related to the productivity of these tropical coastal areas. This spatial analysis suggests that existing protected areas in this region may not include the most critical habitats for snubfin and humpback dolphins. The techniques used here shown relationships between the spatial distribution of the dolphins and environmental features that should facilitate their management and conservation.