Indian estuaries are hypothesized to export a significant amount of nitrogen nutrients to the coastal waters due to the high use of fertilizers. To examine the possible sources of nitrogen nutrients and their modifications within the estuary, a study was conducted by collecting samples at monthly intervals for a period of a year. The river Godavari is the largest monsoonal estuary in India and is fed by monsoon rainfall. Hence the entire estuary is filled with fresh water from July to September (the wet period) whereas saline water is dominant during the dry period. An order of magnitude increase in nitrate concentrations was observed during the wet due to a peak in discharge compared to the dry period. The isotopic composition of nitrogen in nitrate (δ¹⁵N_NO3) was lower during the wet than the dry period and displayed a significant linear relationship with Chlorophyll-a (Chl-a), particulate organic nitrogen (PON) and carbon (POC) indicating that biological process modified their composition. The lower δ¹⁵N_NO3 and higher δ¹⁸O_NO3 values were noticed during the wet than during the dry period. The δ¹⁵N_NO3 versus δ¹⁸O_NO3 plot suggests a possible source of nitrate through the nitrification of soil/sewage-borne nitrogen. The higher δ¹⁸O_NO3/δ¹⁵N_NO3 ratios (>1) were observed during August and September than in other months indicating the occurrence of denitrification during the former months. In contrast, an insignificant change in δ¹⁵N_NO3 and δ¹⁸O_NO3 within the estuary suggested that denitrification occurred upstream and not within the estuarine zone. River discharge brought residual nitrate to the estuary leading to less input of nitrate to the coastal Bay of Bengal than hitherto hypothesized.