The aquatic environment in the Yangtze River Estuary has suffered frequently from harmful algal blooms in the recently years. Reasons are nutrients overloading. This phenomenon is associated with a higher population, more urbanization, manure production and agricultural activities in the Yangtze River basin. Studies had indicated that the diffuse sources from agricultural land dominated the river nitrogen export. My research aims to improve our understanding of (1) the seasonal variation in river export of DIN by source and at the sub-basin, (2) contribution of different cropping systems to nitrogen pollution in the rivers (3) the effect of crop-animal intervention on crop yield and water quality and (4) sub-basin specific management options in crop-animal intervention to reduce water pollution.