The longitudinal variations in the nitrogen (d 15 N) and oxygen (d 18 O) isotopic compositions of nitrate (NO 3 -), the carbon isotopic composition (d 13 C) of dissolved inorganic carbon (DIC) and the d 13 C and d 15 N of particulate organic matter were determined in two Southeast Asian rivers contrasting in the watershed geology and land use to understand internal nitrogen cycling processes. The d 15 N NO 3 became higher longitudinally in the freshwater reach of both rivers. The d 18 O NO 3 also increased longitudinally in the river with a relatively steeper longitudinal gradient and a less cultivated watershed, while the d 18 O NO 3 gradually decreased in the other river. A simple model for the d 15 N NO 3 and the d 18 O NO 3 that accounts for simultaneous input and removal of NO 3 -suggested that the dynamics of NO 3 -in the former river were controlled by the internal production by nitrification and the removal by denitrification, whereas that in the latter river was significantly affected by the anthropogenic NO 3 -loading in addition to the denitrification and/or assimilation. In the freshwater-brackish transition zone, heterotrophic activities in the river water were apparently elevated as indicated by minimal dissolved oxygen, minimal d 13 C DIC and maximal pCO 2 . The d 15 N of suspended particulate nitrogen (PN) varied in parallel to the d 15 N NO 3 there, suggesting that the biochemical recycling processes (remineralization of PN coupled to nitrification, and assimilation of NO 3 --N back to PN) played dominant roles in the instream nitrogen transformation. In the brackish zone of both rivers, the d 15 N NO 3 displayed a declining trend while the d 18 O NO 3 increased sharply. The redox cycling of NO 3 -/NO 2 -and/or deposition of atmospheric nitrogen oxides may have been the major controlling factor for the estuarine d 15 N NO 3 and d 18 O NO 3 , however, the exact mechanism behind the observed trends is currently unresolved.