Water quality of rivers in Japanese domestic dairy and pig raising regions, as well as the groundwater in these regions, was investigated. Regarding the method of disposing livestock excreta, interview results from the livestock production farmers and the results of water quality analysis were evaluated. It is concluded that the rivers and the groundwater were contaminated due to inappropriate disposal methods of the livestock excreta. The concentrations of ammonium nitrogen and nitrate nitrogen in the rivers and groundwater were high. The sludge from the bottom of the rivers was also investigated and bacteria which are characteristic of excreta of dairy cattle and pigs were detected. The above pollutants were, therefore, considered to be of livestock origin.