Intensified agriculture relies on maximizing crop production by using nitrogen and phosphorus fertilizers to overcome nutrient constraints on cultivated plants. Fertilizers are often applied in excess of minimal crop needs in anticipation of higher than average yields when climatic conditions are favorable. Large confined animal operations are expanding and often result in the transport of crop nutrients from grain- to animal-producing areas, causing in regional imbalances in nutrient inputs and outputs. Fertilizer and manure amendments dominate nutrient cycles in agricultural watersheds and losses, that are economically unimportant to farm production, resulting in nonpoint pollution, which directly impairs water quality. Studies in agricultural landscapes show stream, lake, and reservoir fertility increases with cultivation in the catchment. Landscape alterations that accommodate crop and pasture-based operations negatively alter stream habitats and biota. Crop irrigation increases the potential salt accumulation in the root zone and loss of chemicals in return flows. Insecticide use has largely shifted away from persistent compounds to formulations that do not bio-accumulate. Some herbicides are water soluble and persistent resulting in exceedences of human drinking water criteria. Aquaculture operations, a growing segment of the food supply, are a source of organic matter, nutrients, and antibiotics to waters. Many cultured species are not native or are selectively bred and escapes can have irreversible ecological impacts. Blunting the adverse impact of agriculture on water quality is complicated because sources are nonpoint and a large number of producers contribute a small individual share to the overall problem.