Modification of natural coastlines is prevalent as human coastal populations swell and effects of global climate change become clearer. We investigated effects of shoreline hardening and environmental factors on benthic infauna and trophic structure in the Patuxent River, Maryland, a stressed mesohaline Chesapeake Bay tributary. We characterized differences in density, diversity, biomass, and trophic structure for large (>3 mm) and small (>500 ?m) infauna adjacent to natural marsh, riprap, and bulkhead (i.e., seawall) shores throughout the river. Akaike information criterion model comparisons were used to assess the evidence for differences in benthic infaunal structure using primary (shoreline type) and secondary (e.g., sediment grain size, predator abundance) variables. There was strong evidence for secondary factors to explain reduced biomass of infauna adjacent to developed shorelines. For large infauna, evidence suggested that shorelines with riprap had reduced diversity, and with bulkhead had increased diversity. Increased wave energy and chlorophyll-a were associated with high densities for both size fractions riprap shorelines. Trends suggested high biomass and more carnivores, omnivores, and deposit feeders adjacent to natural marshes, compared to low biomass and more filter feeders at developed shorelines. While similar studies in lower Chesapeake Bay systems have shown clear effects of shoreline type on benthic communities, the extensive development in the Patuxent River may contribute to larger-scale stress, yet some shoreline-specific effects were detected. Non-parametric tests revealed differences in infaunal communities by shoreline type and river zone. Thus, the benthic community in this estuary is driven by local shoreline effects, as well as large-scale physical and biotic factors.