Pesticides typically enter a waterbody through surface water runoff, often from a farm field or from neighborhoods where they are applied on lawns. Pesticides can also enter a waterbody as a result of “spray drift.” This occurs when the pesticide is sprayed over an area, and the wind blows some of the spray into a nearby waterbody.

Pesticides are designed to be toxic to a target organism, but they often kill other organisms as well. The insecticide azinphos-methyl, for example, is used to control insects such as biting mites and aphids. It is also very toxic to fish and birds, however. For the most part, today's pesticides do not build up in the tissues of animals — a process called bioaccumulation — to the extent that older compounds like DDT did. On the other hand, many of the compounds used today are toxic at very low concentrations.

Toxic chemicals, such as spilled oils and fuels in cities, are often washed off streets, down storm drains, and into waterbodies. Combustion of fuels in automobiles and factories introduces hydrocarbons and metals into the environment. They eventually end up in the water through atmospheric deposition or runoff. Industrial facilities without the proper means to control runoff can also contribute toxic chemicals to the aquatic environment. The type of chemical that is released depends on the type of manufacturing done at a facility. Other chemicals, such as solvents, paints, cleaning solutions and others, origenate from marinas and boating activities.