Estuaries are critical aquatic environments that are used by many fish during their life cycle. However, estuaries often suffer from poor water quality as a result of anthropogenic activities. Fish diversity studies in estuaries are common, although few have examined whether correlations exist between water quality, metal contamination and fish assemblages. In the present study we investigated the effect of abiotic conditions, heavy metals and estuary characteristics on the abundance, diversity and composition of fish in four intermittently open estuaries along the Illawarra coast of south-eastern Australia. The heterogeneity of environmental conditions was reflected in the fish assemblages in each estuary. Environmental variables predicted fish species composition, and estuaries in particularly poor condition contained few species (estuarine residents) in high abundance, indicating their ability to acclimatise and survive in conditions that are hostile to other species. Overall, these findings demonstrate that estuarine fish assemblages may be useful indicators of estuary condition and reveal the importance of managing anthropogenic activities in the surrounding catchment to improve water quality so that biodiversity of fish can be restored in these estuarine environments.