This study examines global zoogeographic patterns of estuary-associated fishes using meta-assemblages compiled at the marine ecoregion scale. The classification of biogeographic regions based on estuary-associated fish species is assessed in relation to marine and freshwater zoogeographic patterns. Historical (palaeobiogeographic) and contemporary environmental factors that contribute to the establishment and maintenance of these regions are also discussed. Global patterns in estuary-associated fish species richness demonstrated that tropical ecoregions are more diverse and richer in species than temperate ecoregions; the tropical Indo-Pacific and the tropical western Atlantic were two major centres of high global species richness. Multivariate analyses identified several ecoregion groupings that broadly corresponded with both freshwater and marine biogeographic regions. These groupings could also be related to global marine palaeobiogeographic processes such as the closure of the Tethys Sea linkage during the Cenozoic as well as contemporary factors such ocean currents, upwelling areas and climatic factors, particularly rainfall and runoff.