Bathymetric features modify coastal habitat availability and quality across seascapes, but how these features change ecological value remains poorly quantified in many settings. We surveyed fish assemblages in remnant shellfish reefs and unvegetated control sites in South-East Queensland with Stereo Remote Underwater Video Systems (Stereo-RUVS) and quantified detailed three-dimensional terrain using sonar-derived bathymetric maps to test how seafloor bathymetry influences shellfish reef nursery value. Juvenile density of harvestable fish species were converted into financial value, according to market cost and fisheries contribution. We identified significant effects of shellfish reef complexity on fish. Here, variation in reef characteristics (e.g., vertical relief), seafloor terrain (e.g., slope), benthic composition (e.g., algae cover) and seascape connectivity (e.g., distance to mangroves) explained significant changes in fish diversity and nursery habitat value. We also found mediating effects of benthic composition and seascape connectivity on these patterns. The next phase of this project will expand this nursery value methodology into multiple intertidal habitats to compare differently structured habitats (i.e., low structured seagrass compared to higher structured shellfish reef). This research further supports incorporating detailed three-dimensional bathymetry into coastal conservation, monitoring and restoration efforts to help improve nursery value throughout the seascape.