Recovering populations of large predators are indicative of productive ecosystems, and also bring with them crucial ecosystem services and oft cascading trophic effects to biological communities. Understanding the role of predators in shaping ecosystem processes is critical for effective marine resource management and therefore ecosystem conservation, a critical issue on highly populated and human-impacted coastal areas. We investigated the trophic dynamics of two sympatric predators, Australian and long-nosed fur seals, using DNA metabarcoding techniques to analyse their diets across multiple locations of recolonisation on the south coast of NSW. To evaluate the potential for localised effects of predator aggregation sites on fish and temperate reef communities, we also undertook surveys at fur seal haul-out sites and sites of relatively low fur seal activity. We found considerable overlap of key prey groups in the diets of both seal species across sampling time at the most peripheral haul-out site (Jervis Bay) and strong trophic linkages with coastal ecosystems due to the high prevalence of benthic, demersal and reef-associated prey. In contrast, diet composition of both seal species from the breeding colony (Montague Island) were more consistent with foraging patterns for both species from more central parts of their geographic range. These results suggest there may be different trophic interactions at newly recolonised sites compared to established colonies, with different outcomes for marine communities and which may impact the way that we manage dynamic species and communities. We detected some localised effects of fur seal haul-out sites on temperate reef communities, however, effects were not as strong as expected, indicating that local initiatives for marine resource management are not necessarily severely compromised by recovering populations of predators. Finally, there was considerable overlap in predator diets with important fisheries on the east coast of Australia, highlighting a need to better evaluate this overlap and complex trophic interactions between multiple key players in ecosystem processes.