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Nitrates and Phosphorus are the two main contaminants that pollute the Mississippi River Watershed. This nutrient pollution comes from a surplus of phosphorus and nitrogen, both of which occur naturally in water and air. In the Upper Mississippi River Basin farmland, nitrate fertilizer has been overused in farming, with the high demand for corn as a contributing factor. Corn, which is used to make ethanol for biofuel, has become the number one crop in the farmland that drains into the Mississippi River. Soybeans are another crop in the Upper Mississippi River Basin farmland that drain into the watershed, and nitrates are the main fertilizer used on soybeans and corn.

A variety of changes are needed in the agriculture industry to reduce the pollution from over fertilizing. One solution for nitrate reduction is to plant an alternative crop through crop rotation, such as legumes. Legumes are capable of nitrate fixation, which causes the plant to have a reduced need for nitrate fertilizer. Nitrate drainage is then reduced going into the watershed because legumes do not require the high amounts of fertilizer that are needed for corn and soybeans. Other alternative plants that can be used in crop rotation are miscanthus and switchgrass. These crops effectively reduce the flow of nitrates going into the Mississippi River Basin.

Conservation practices can be used as alternative crops to reduce phosphorus and nitrate pollution in the River. They are necessary since nutrient pollution affects humans and aquatic life in the waterways leading to the Watershed along with the coast. The Gulf of Mexico receives the greatest damage from the pollution. Normal algae growth in water is needed to provide food for fish and other water organisms, but algae can grow too quickly because of the excess nitrogen and phosphorus going into the Mississippi River Basin. The overgrowth produces an algae or algal bloom, which reduces the amount of oxygen in the water. The depleted oxygen levels kill the aquatic life in the Gulf of Mexico, and it can make fish and other aquatic life sick. Humans can be affected if they drink water or consume fish and other aquatic life that have been contaminated with bacteria or other toxic substances from the algae blooms. Shellfish contamination from the algae occurs easily, and it can be very dangerous for human consumption and cause stomach issues and rashes.

Millions of people throughout the United States have a water source connected to the Mississippi River Watershed because the basin is connected to groundwater, well water, and other water supply tributaries throughout the country. The watershed also serves as largest drainage system in the country. Drinking water from the basin that is polluted by nitrates and phosphorus can cause serious injury to anyone who consumes it, especially young infants. The chemicals that are used to treat the polluted water are very dangerous. These chemicals cannot be avoided since there are no real alternatives to treat the polluted water. The contaminated water source also harms forests that are located in the basin, and animals can be affected if they consume water or plants that have been contaminated by the nutrient pollution. Nitrates and phosphorus also pollute the air, and if the air is polluted, eventually the contamination will fall back to the earth and the waterway making its way through the basin.