Extensive datasets document the distribution and composition of benthic macrofauna in some estuaries, yet their impact on carbon cycling remains poorly quantified. To address this, we investigated (1) how water chemistry and sediment composition correlate with benthic biomass distribution and (2) the contributions of benthic macrofaunal carbon fluxes to estuarine carbon budgets. We analyzed 8,128 benthic samples collected from Chesapeake Bay (1995–2022) and used generalized additive models to relate observed and modeled environmental variables to the biomass. We also estimated their associated carbon fluxes (calcification and respiration rates) using empirical relationships. The highest biomass was found in the upper Potomac River Estuary and Upper Bay; moderate dissolved oxygen, low salinity, and high nitrate concentrations were the clearest predictors of these zones (explaining 52 % of the deviance in biomass). Low surface NO₃^- concentrations within the estuary coincide with high inputs of allochthonous particulate organic carbon (POC) from riverine sources; this POC be the primary food source supporting high biomass zones. In the oligohaline Upper Bay, benthic macrofauna respire 17–50 % of total organic carbon available in that region, whereas their contribution is lower downstream. Moreover, the estimated benthic macrofaunal CO₂production rates from respiration and calcification rates in the Upper Bay (205±70 g C m^-2 yr^-1) exceeds estimated outgassing (74.5 g C m^-2 yr^-1), suggesting benthic macrofauna contribute significantly to air-sea gas exchange. The explainable spatial distribution of biomass and major role in estuarine carbon cycling highlight the importance and feasibility of incorporating the impacts of benthic macrofauna into numerical models. Refining these models could improve predictions of estuarine responses to natural and anthropogenic changes.