Water bodies' nitrogen contamination has become more and more serious due to the effects of the intensive development of industry and agriculture. It is important to use nitrogen stable isotope data to identify the nitrogen pollution sources and study the nitrogen cycle of water bodies. This article gave an overview of basic information as follows: 1) introducing the nitrogen stable isotope, nitrogen cycle and the fractionation factors; 2) comparing the analysis techniques of nitrogen isotope separation, enrichment, transformation of different forms; 3) discussing the application of nitrogen stable isotope in natural nitrogen cycle of different water types, nitrogen pollution sources justification, the biogeochemical processes in water bodies, and the eutrophication; 4) summarizing the methods of identifying denitrification, the two attenuation mechanisms of nitrate pollution, i.e., denitrification and dilution; 5) pointing out the deficiency of the current research.