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The agricultural use of fertilizers is not regulated; however, water runoff from agricultural properties is subject to regulation. Fertilizer, when applied incorrectly, can be easily moved by irrigation or stormwater runoff and can make its way to streams, rivers, lakes, oceans, and into the groundwater. Utilizing best management practices (BMPs) for nutrient management can significantly reduce the potential for water pollution.

Irrigation and stormwater runoff from agricultural properties is regulated under the Conditional Waiver for Discharges from Agricultural and Nursery Operations, or Ag Waiver. The County of San Diego has stormwater pollution regulations that may affect agricultural operations. Certain classes of agricultural operations, such as dairies, may be regulated by National Pollutant Discharge Elimination System program.