Confined animal production in the U.S. and its associated discharge of manure nutrients into area waters is considered a leading contributor to current water quality impairments. A common option to mitigate these impairments is to limit land application of manure. This paper evaluates the implications of alternative land application constraints for U.S. agriculture and the environment at the regional and sector level. The results suggest that when these constraints are particularly binding, due to minimal acceptance of manure as a substitute for commercial fertilizer, potentially large and unanticipated changes in returns to agricultural production and water quality may occur. Furthermore, we find that some of the cost of meeting the land application constraints will be passed on to consumers through higher prices and to a portion of rural economies through lower production rates and labor expenditures.