Nitrogen (N) is widespread in nature and is a fundamental element in the composition of amino acids, playing a crucial role in living organisms. However, increased human activities have dramatically altered the global nitrogen cycle, especially in Chinese surface water systems, leading to eutrophication, harmful algal overpopulation, ecological stress, and heightened greenhouse gas emissions. This review examined nitrogen cycling in major Chinese watersheds from three perspectives. Initially, the current pollution status of nitrogen pollution and its spatial and temporal distribution patterns in major river basins in China were delineated. Subsequently, we concentrated on summarizing the latest insights into the significance of microbial-driven nitrogen transformations in Chinese major rivers, including nitrogen fixation, nitrification, complete ammonia oxidation, denitrification, dissimilatory nitrate reduction to ammonium, and anaerobic ammonia oxidation. Finally, future attention that should be paid to the response of nitrogen-cycling processes to climate change and the contribution of chemoautotrophic nitrogen-cycling processes in watersheds, as well as the importance of keystone species and assembly mechanisms in microbial communities, to forecast the response of the nitrogen cycle to future environmental changes in major Chinese river basins was discussed.