Coastal development affects estuarine resources by severing terrestrial-aquatic linkages, reducing shallow water habitats, and degrading ecosystem services, which is predicted to result in measurable declines in nekton community integrity. We assessed the effects of landscape features on nearshore habitats and biological communities, relating subtidal habitat, shoreline condition, upland land use and nearshore fish communities in a Chesapeake Bay tributary, the James River, Virginia. Both upland development and the placement of erosion control structures on the shoreline were associated with reduced fish community integrity, and shoreline alterations were linked with the amount of subtidal structural habitat in the nearshore. Ecological thresholds in nekton community integrity were evident at \u3e= 23% developed land use within 200 and 1000 m buffer increments. Nekton assemblages at sites with low development (\u3c 23%) and natural or riprap shorelines were different from all other combinations of altered conditions (low development with bulkhead, and high development with riprap or bulkhead). Species composition along natural or riprap revetment shorelines with low upland development tended to be diverse and inclusive of tidal marsh species, while highly developed sites or bulkhead shorelines were dominated by a few generalist species. The complex interaction between watershed (both nearshore and inland) and shoreline development presents a unique challenge for coastal planning. Alternate moderating approaches for coastal development may include preservation of riparian buffers, the placement of living shorelines for erosion control where appropriate, and development of targeting tools to identify landscapes near an ecological threshold