Nature reserves are created to conserve biodiversity and restore populations of harvested species, but it is not clear whether this strategy is successful in all ecosystems. Reserves are gazetted in estuaries to offset impacts from burgeoning human populations, however, coastal conservation cannot be optimized because their effectiveness is rarely evaluated. We surveyed 220 sites in 22 estuaries in the Moreton Bay Marine Park, Queensland, Australia, including all six current estuarine marine reserves within the park. Fishes were surveyed using one hour deployments of baited remote underwater video stations twice at each site over consecutive days. We show that although the estuarine reserves in Moreton Bay contain a significantly different fish community, they fail to enhance the abundance of harvested fish species. We posit that performance is limited because reserves protect unique spatial features, or conserve narrow estuaries with weak connections to mangrove habitats and the open sea. Consequently, reserves as currently positioned protect only a subset of potential environmental conditions present for fish within the region, and potentially support residual estuarine habitats (i.e. expansive intertidal flats or shallow creeks) which are not particularly significant to either fish or fishers. We argue that reserve effectiveness can be improved by conserving deeper estuaries, with diverse habitats for fish and strong connections to the open sea. Without incorporating these critical spatial considerations into estuarine reserve design, estuarine reserves are doomed to fail.