Excess nutrient (N and P) loads are recognized as the major cause of serious water quality problems in China. River systems play a very important role in nitrate (NO3 (-)) transportation and transformation in the aquatic environment. To understand and clarify the sources and processes affecting NO3 (-) in river basins, we have examined spatial and temporal variations of concentration and dual-isotopic composition of NO3 (-) in the dam-controlled Jialing River, a major tributary of the Yangtze River where land use is dominated by agriculture. Water samples were collected in July 2008 and February 2009 from the main channel of the Jialing River and its major tributaries. The delta N-15 and delta O-18 of NO3 (-) range from 1.5 to 11.0 aEuro degrees (average 6.2 aEuro degrees) and -5.0 to 11.1 aEuro degrees (average, 1.6 aEuro degrees), respectively. NO3 (-) isotope data and delta O-18 of water interpreted in combination with hydrological and chemical data suggest that most of the NO3 (-) input is from nitrification during the rainy season, and discharge of sewage and manure in the upper course and from cities accounts for much of the NO3 (-) load during the dry season. The construction of cascade dams has led to retention of Si and a decrease in the Si/N ratio, implying that assimilation and/or denitrification may significantly affect NO3 (-) in the dam area, as demonstrated by NO3 (-) and dissolved Si concentrations, and and values. This study indicates that dual-isotopic data can be used to identify NO3 (-) pollution sources and the processes NO3 (-) has undergone during its retention and transport in the watershed of the dam-controlled Jialing River.