With increased concentration of livestock numbers and operations into smaller geographic areas, particularly confinement animal feeding operations (CAFOS) for cattle and swine (and also poultry), there are concerns surrounding the impacts of animal agriculture on the quality of our natural resources. Storage and land application management practices of manure generated by these operations can affect air and water quality. Manure management plans written to provide nutrients at rates necessary for crop production can sometimes result in over application of phosphorus (P) when the rate of manure application is based on the nitrogen (N) needs of the crop/rotation. This is particularly true for continuous com and for com rotated with soybeans where the N needs of the com and soybeans are both met with manure applications. This over application of P leads to surface water quality and possible P leaching concerns. These concerns, how they are affected by P fate and transport, and how management practices affect P fate and transport, are the subjects of this paper.