Comprehensive bimonthly field surveys were carried out from September 2000 to June 2002 to study the seasonal dynamics and the inter-annual variability of dissolved inorganic nitrogen (DIN; nitrate, nitrite and ammonium) and dissolved inorganic phosphorus (DIP) in a subtropical mountain river system, the Danshuei tributary, the largest urbanized estuarine system in Taiwan. The headwaters were found to be well aerated, saturated with oxygen, with low ambient DIN (<9 μM) and DIP (<0.2 μM) concentration. As the river flows through the city of Taipei, the river becomes hypoxic because re-aeration rates cannot keep up with elevated oxygen consumption, and the concentrations of DIP (7.53 μM) and DIN (∼390 μM) increase drastically. Conservative mixing was mostly observed for silicate while DIP and DIN mostly showed non-conservative removal characteristics. Silicate originates from weathering and erosion of bedrocks in the watershed, whereas nitrogen- and phosphorus-bearing nutrients come mainly from urban discharges. Ammonium is the predominant dissolved nitrogenous species, ranging from 10 to 1000 μM. The nutrient chemistry is complex and dynamic due to anthropogenic perturbations and reactions in the tidally mixed zone of strong redox gradients. On average, the annual loading rates of dissolved phosphate and dissolved inorganic nitrogen from the Danshuei River to the ocean are 0.1 and 3.2 Gmol/year, respectively, which represent 0.1% and 0.2% of the world's total river discharge of dissolved inorganic nitrogen and phosphate.