Objective of this study was to understand farmer's management practices related to water quality and sanitary issue in order to assess the risks of these practices especially in the Upper Ouémé Delta. All the data related to this investigation were collected by field observations, interviews, surveys of farming households and focus groups. T he surveys were conducted with 387 farmers belongs to three districts of southern Benin (Bonou, Ouinhi, and Zagnanado). Results of study revealed that 97.48%, 57.78%, 76% of farmers respectively of the Bonou, Ouinhi, and Zagnanado districts grow food crops. Among these, 2.53%, 42.22% and 24% cultivate cash crops such as cotton and oil palm. According to survey results, soil conservation and tillage practices are widely practiced. Further, crops rotation and fallow are widely practiced in all studied districts and 84.84% of the surveyed farmers use chemical pesticides to maximize crop yields. Among these, only 2.32% farmers used aqueous extracts of Azaradichta indica leaves for protecting crops against pests. The sources of the environmental risk are the type of chemical product on pesticide used, its toxicity, the parallel circuits of provisioning of pesticides, and the lack of use of protection clothes for spraying these products. This practice allowed ground and water pollution and leads to public health matter. A promotion of good practices is essential for a durable exploitation of the natural resources of the Upper Delta of Ouémé area.