According to the Environmental Protection Agency (1993), agriculture may be one of the greatest contributors to water pollution in the United States. In addition, the California State Water Resources Control Board has identified the Pajaro River Watershed as having significant water quality impairments. The Pajaro River Watershed, several of its tributary streams and the Watsonville Sloughs, are now listed on the Regional Water Quality Control Board (RWQCB) prioritized 303d list of water bodies impaired from nutrients, sediments, and pesticide pollution.
As runoff water and sediment is lost from the agricultural lands of the Pajaro Watershed, it is transported to the Sanctuary waters, often also carrying with it non-point source pollution originating from urban streets and stormwater drainages. These factors contribute significantly to the degradation of the watershed. While the water quality and ecological integrity of the watershed and the Bay depend upon stewardship from both agricultural and urban communities, the long-term viability of communities themselves relates closely to water quality and the general health of the watershed.