Connectivity between land and sea through the movement of species, energy and nutrients means that land-based impacts can affect the structure and functioning of nearby coastal ecosystems. As the interface between land and sea, estuaries are often faced with increasing pressures from catchment modifications (e.g. the removal of terrestrial vegetation) which can alter the overall health of estuaries (e.g. the degradation of coastal water quality due to an increase in terrestrial runoff) and change the value of habitat for many marine species. These landscape-scale impacts can, however, be mediated through variations in the context and connectivity of seascapes (e.g. greater extent of vegetated ecosystems help to filter nutrients). We surveyed fish across five estuaries over four years using underwater videography and sought correlations between fish biodiversity and abundance with variables indexing catchment land use, seascape connectivity, and coastal water quality. Fish assemblages were more abundant and diverse at sites which had lower chlorophyll-a concentrations and were nearer to the estuary mouth, in conjunction with catchments containing higher percent of natural land and heterogenous seascapes. Sites with lower concentrations of chlorophyll-a supported indicator species from more diverse functional groups that had greater fisheries values, in comparison to indicator species from sites with high concentrations of chlorophyll-a. This research can help direct coastal management to better prioritise management in coastal ecosystems, thereby enhancing fish richness and abundance, functional group richness and fisheries value.