Benthic macrofauna can play an important role in facilitating some of the microbial mediated processes of nitrogen cycling in estuarine sediments. Declines in benthic macrofauna, like polychaete worms, have been attributed to long-term increases in bottom water hypoxia in Chesapeake Bay. Utilizing a large monitoring dataset including benthic macrofaunal abundance, biomass, and concurrent measures of environmental parameters, I examined how environmental conditions regulate the densities of opportunistic polychaetes in a mesohaline estuarine system. This analysis points to a benthic community dominated by euryhaline, opportunistic polychaete worms (M. viridis, S. benedicti, H. filiformis, A. succinea) which have well adapted but varying responses to hypoxia and other stressful conditions. Results of two laboratory experiments with the opportunistic polychaete Alitta (Neanthes) succinea were used to quantify the short-term influence of density and size of surface-feeding polychaetes on sediment-water fluxes of inorganic nitrogen under varying oxygen conditions. Polychaete enhancements of O₂ and nitrogen fluxes were strongly correlated with total animal biomass. Solute fluxes were stimulated by presence of both larger and smaller worms, but per capita effects were greater for the deep-burrowing larger polychaetes. Utilizing a unique large-scale monitoring dataset collected in the Chesapeake Bay, I employed Classification and Regression Tree (CART) and multiple linear regression (MLR) analyses to assess the relationship between benthic biomass and NH₄+ efflux within different regions of the estuary by season. In addition to labile organic matter, oligohaline and mesohaline tributary temperature and salinity control the rate of nitrogen cycling and benthic macrofaunal biomass. In deeper regions of mesohaline tributaries and the mainstem Bay, dissolved oxygen was found to be the dominating parameter regulating sediment nitrogen pathways as well as the structure of the benthic macrofaunal community. With increased macrofaunal biomass, spring regressions indicated an enhancement of NH₄+ efflux. In contrast, fall regressions indicated the enhancement of fixed nitrogen removal from sediments. Summer data lacked a significant relationship, but high NH₄+ effluxes under hypoxic/anoxic conditions suggested dissolved oxygen is the primary driver of summer nitrogen cycling. This study, using field and laboratory data, concludes that a complex balance between seasonal and regional dissolved oxygen, temperature and salinity conditions shape not only the benthic community but also the relationship between macrofaunal biomass and sediment nitrogen flux in this eutrophic estuarine system.