Agriculture has dramatically increased the efficiency of grain and protein production for the world’s growing population for a given unit of land area. In most cases, this increase has been achieved through crop and animal breeding, increased use of fertilizers, while using less land area. With intensification of production systems, there has been a greater frequency and severity of water quality impairment associated with nonpoint discharge of nutrient from agriculture to surface and ground waters. This chapter reviews the causes of these impacts on water quality and how future water quality problems could be mitigated. The chapter examines the cycling, fate, and transport of phosphorus in agriculture, remedial measures and the legacies of past management. Finally, the chapter looks ahead to future research trends in this area.