Hybrid shoreline stabilisation using rock fillets has successfully facilitated mangrove establishment along eroding estuarine shorelines in New South Wales, Australia. This study compared mangrove structure, benthic macrofauna, and nekton assemblages in hybrid mangroves to nearby natural fringing mangroves across multiple estuaries. Hybrid mangroves exhibited higher tree and seedling densities but similar macrobenthos abundance to the natural mangroves. However, differences in macrobenthos composition, particularly among crab and polychaete species, varied across estuaries and between shorelines with different mangrove cover. However, mangrove cover had little influence on nekton species utilisation of hybrid mangroves. Fish abundance was generally higher in hybrid mangroves than in natural ones, likely due to the hydrodynamic shielding and additional refuge provided by rock crevices. When designing hybrid living shorelines, it is essential to consider recovery timelines and potential trade-offs in ecological processes, which depend on local species pools and environmental conditions. Where natural mangrove establishment is unlikely due to high wave energy, rock fillets can serve as an effective approach to reduce lateral erosion while providing critical estuarine habitats.