Coastlines worldwide are being altered due to shoreline hardening and stabilization and while highly altered systems are subject to change, variability exists in how shoreline hardening affects benthic communities depending on the landscape features of the system and regional production. Oyster reefs have been used to stabilize shorelines and offer a potentially positive effect on shoreline communities. In a field survey, we used 29 sites throughout the Lynnhaven River System, a highly developed yet productive subestuary of Chesapeake Bay, to determine effects of shoreline type (natural marsh, oyster shell reef, rip-rap, and bulkhead), sediment characteristics (grain size and total organic carbon and total nitrogen), and predators on benthic infaunal density, biomass, and diversity. An information-theoretic approach was used to determine which of several hypothesized Generalized Linear Models were supported by the data. Shoreline type was the best predictor of benthic infaunal density, with oyster reefs having the highest benthic density and bulkhead the lowest. In contrast, sediment characteristics and predators were the best predictors of benthic infaunal biomass and diversity. The Lynnhaven system is shallow (~2.5 m), and nearly 78% of the shoreline is natural marsh, which promotes high regional benthic productivity that may mask small-scale effects of shoreline stabilization on infauna. Our findings contrast with previous studies in moderately productive systems where altered shorelines had substantial direct effects on the benthos, suggesting that further studies need to take place across various systems among a range of upland usages to help clarify the impact of local shoreline stabilization versus regional watershed usage on benthic communities. Our results highlight that high ecosystem productivity is important for resilience to local shoreline modification.