Climate change and urbanization of coastal areas are impacting estuarine habitats globally. While these regions are important for the early-life development of many aquatic species, links between habitat use and foraging ecology are not well known. Thus, it is essential to understand the importance of threatened habitats for animals inhabiting estuaries to promote their conservation and improve ecosystem management. This study examined the importance of estuarine habitats as feeding grounds for juvenile bull sharks (Carcharhinus leucas) in the Clarence River, a nursery area where the species is targeted by commercial fisheries in New South Wales, Australia. Juvenile sharks (n = 54) ranging from one to ∼6.5 years-old, together with particulate matter and several primary producer species of mangrove and saltmarsh, were sampled for δ13C, δ15N and δ34S stable isotopes. Bayesian mixing models and a Generalized Additive Mixed Model were used to investigate the contribution of estuarine habitats to the diet of bull sharks and changes with growth. The importance of resources consumed from within mangrove habitats for juvenile bull shark resource use was minimal but slightly increased with age, with younger sharks (<2.5 years) relying on prey feeding on sources derived from particulate organic matter, while older juveniles (4–6.5 years) preyed on species that relied mostly on threatened saltmarsh habitats. Our findings highlight the important linkages between habitats of conservation concern and species redistribution in response to climate change, particularly as the animals could be moving towards new areas lacking suitable estuarine habitats.