Abstract: Correlative statistic data about the issue of agricultural non-point source pollution in Fujian province during 1995-2004 were analyzed in the study. The changing status of the water quality of the 12 main water systems, chief lakes and reservoirs and seawater near coast in Fujian province were expatiated. Results showed that: the environmental quality of water area in Fujian province had been continuously deteriorated since 2002; the proportion of Ⅰ~Ⅲ types water in the 12 main water systems and chief lakes & reservoirs was declined from 90.6% and 77.8% in 2002 to 83.6% and 36.4% in 2004, respectively; the proportion ofⅠandⅡtypes water in the seawater near coast was declined from 47.3% in 2002 to 32.3% in 2004. Moreover, agricultural non-point source pollution factors which causing the deterioration of water environmental quality were analyzed, and those primary factors included chemical fertilizer, pesticide, farming plastic film, livestock and birds raising, water and soil erosion, aquiculture. Finally, prevention and cure countermeasures to control agricultural non-point source pollution in Fujian province were put forward, those mainly included: perfecting agriculture legislation and intensifying management measures, strengthening research to technique of least devotion of agriculture chemical substance, developing all-purpose and synthetical use of dejection of livestock and birds, developing ecological agriculture and organic agriculture, advocating cleansing production and containing agricultural non-point source pollution, reasonably putting in fish feed and medication and reducing their losses rate.