To test how benthic biogeochemistry responds to changing nutrient availability and estuary trophic state, I conducted mesocosm and field experiments. In the mesocosm experiment, sediment cores from eutrophic and oligotrophic estuaries were incubated under high or low nutrient levels. Net production rates were greater in eutrophic vs. oligotrophic cores while respiration rates were greater in high nutrient treatments, indicating that sediment metabolism was affected by trophic history and nutrient availability. Sediment organic matter (SOM) composition was insensitive to the nutrient treatments but varied with trophic history as carbon : nitrogen ratios were lower, δ15N was higher, and algal and bacterial fatty acids (FAs) were more abundant in eutrophic sediments. In the field experiment, intact cores were reciprocally transplanted between eutrophic and oligotrophic estuaries and changes in SOM composition were followed over four months. SOM responses were more dramatic in cores transplanted to the oligotrophic vs. eutrophic estuary. In sediments moved from the eutrophic to oligotrophic estuary, carbon and nitrogen content as well as abundances of algal and bacterial FAs fell within one month. Conversely, sediment δ15N increased sharply while algal and bacterial FAs rose slightly in cores transplanted from the oligotrophic to eutrophic estuary. Different SOM responses between the experiments were likely due to direct vs. indirect effects of nutrient enrichment. Nutrient levels were manipulated in the mesocosm experiment while the estuaries differed in nutrients, macroalgal biomass, benthic animal communities, and oxygen levels. Consequently, sediment biogeochemical responses to watershed nutrient mitigation will likely follow broader changes in estuary habitat quality.