Implementing the Water framework directive requests that regulator at local scale can choose among all potential measures those that are the most effective for water pollution mitigation. On the watersheds, the pollution in water is the result of point and non-point sources. For the latter, the difficulty in measuring the individual emissions renders the design of mitigating policies particularly uneasy. Non point source pollutions from nutrients, pesticides or hazardous substances in groundwater exhibits specific characteristics such as a long lag between human polluting actions and the resulting pollutions level that can be measured in groundwater. This chapter consist in guidelines to compare good farming practices at the watershed scale. It focuses on main key elements useful for decision making (BMPs and critical areas definitions, cost/effectiveness approach, acceptability and integrative analysis grid).