Estuaries are becoming increasingly threatened by human activities and there is growing appreciation that the management of estuaries must consider impacts of multiple human stressors. Cumulative impact maps have become a popular tool to identify the distribution and intensity of multiple human stressors in estuaries. Few studies, however, have demonstrated strong correlations between cumulative impact maps and changes in ecosystem condition questioning their use for management. Here, we developed a cumulative impact map for Posidonia australis in Pittwater, NSW, Australia, using spatial data on known stressors to seagrass including water quality, boat moorings, jetties and vessel traffic. We then tested how well cumulative threat scores explained changes in Posidonia australis cover between 2005 and 2019 measured using aerial imagery. Posidonia australis cover increased in areas where cumulative effect scores were low (<4), while declines were observed in areas where cumulative effects scores were high (>4). Using baited remote underwater video we surveyed fishes over seagrass and bare sediments to quantify how changes in seagrass area may be influencing estuarine fish assemblages. As expected, seagrass contained a distinct assemblage of fishes compared to bare sediments. On bare sediments the abundance of sparids (yellowfin bream, tarwhine and snapper) were positively associated with distance to seagrass. Our results demonstrate the negative impact of multiple stressors on Posidonia australis area in Pittwater, which has consequences for estuarine fish biodiversity and the abundance of targeted fishes. Our results suggest that management actions aimed at reducing or limiting cumulative effects to low and moderate levels will help conserve Posidonia australis populations and their associated fishes in Pittwater.