Phosphorus from agricultural non-point sources has been identified as the main cause of freshwater eutrophication throughout the world and contributes a large share to the water quality deterioration. With excessive amount of phosphorus being input to the agro-ecosystem, the accumulation of P in cultivated soils has increased the potential for P loss in agricultural runoff and drainage. This paper attempts to summarize the research activities focused on the build-up of P in soil, the interaction of P with soils and its transport in surface and subsurface drainage. Phosphorus indexing system (PIS) used for identifying sites vulnerable to phosphorus loss in agricultural runoff is introduced. Widely practiced mitigation options include untrient budgeting, input management, soil conservation, land use management and the establishment of vegetated riparian zones, buffer strips and sedimentation ponds which have been proved to be very cost effective in a Chinese context.