Ongoing climate change and anthropogenic activities are introducing stressors that affect the structure and function of coastal ecosystems. This paper focuses on the fluvial fluxes and estuarine transport of nutrients from a tropical river (Mahanadi River) in Northeastern India and compares select nutrient and water quality parameters between 1983 and 2008. This estuary acts as a perennial source of CO2 with a net annual flux to the atmosphere of about 135 tons. The non-conservative fluxes showed a net annual removal of 650 and 140 tons of phosphorus and nitrogen from the water column, respectively. Negative biogeochemical feedbacks that decreased the availability of N and P in 2008 relative to 1983 levels indicate major changes in biogeochemical responses towards fluvial fluxes of nutrient.