The purpose of this paper is to study the application of HACCP principles in dairy production systems for mitigation of potential water related hazards by control measures and legislation applicable at farm level. HACCP logical sequence approach including some principles of environmental risk assessment was the method used for the present study (FAO/IDF, 2004;Horchner et al., 2006). Literature review, farms visits, interviews, informal questionnaires and confirmation on site of the gathered information were the prerequisites of the study. Four flow diagrams in SA and three in Benin were drawn to describe the 11 steps relating the activities of the seven types of dairy farming systems recorded altogether in these countries (FAO/IDF, 2004,McCrindle, 2007). From the flow diagrams, almost three groups of 30 potential hazards were identified. Biological, chemical and physical hazards were characterized and their effects described according to the source, pathways, mechanisms, of water pollution. It was noticed that water use during farming activities is linked to the number of animals and is an important factor to qualify the magnitude of the risk of water pollution. Critical Control Points (CCPs) were identified. In SA, national legislation includes legal prerequisites for commercial dairy farming systems (SA GOVERNMENT 2005, 2006, 2007). Although water resources policies, strategies, legislation and management are strongly established, their implementation does not clearly include dairy by-products. In Benin dairy production strategy and development started in 2000. Basic legislation relating water resources is being updated. In commercial farming systems (F1 and F2 in SA), F7 in Benin, biological and chemical potential hazards are the main threat to water quality. Direct or indirect source of contamination due to manure, feces, urine, chemicals and stock remedies, waste water, occurs through husbandry practices (milking), pasture and housing. In SA, farmers are aware of International dairy standards, norms and practices such as GAP, GMP and GHP even if the practices are not completely respected. HACCP is not well yet well implemented at producer level althougth some commercial dairy processors have started the implementation of the system (FEDICS, 2004, CEBENOR, 2007). Environmental care (CCP11 and CCP12) are the main critical control points recorded which are not mitigated by the national legislation in both countries. In regard to traditional farming systems (F3, F4) and in SA, (F5, F6) in Benin, national legislation does not include prerequisites for biological and physical hazards; these are the main threat of water pollution and are due to direct or indirect contamination through drinking and grazing. Chemical hazards are not important because inputs of stock remedies are low in these systems. Farmers are not aware of International dairy standards, norms and practices such as GAP, GMP and GHP which are fairly respected. HACCP is unknown at producer level. CCPs relating animal treatment and care are partly mitigated by the national legislation. Stock remedies, drugs residues and Pharmaceuticals are controlled in both countries although Benin faces the introduction of uncontrolled veterinary drugs through illegal frontiers. The majority of the CCPs are not completely mitigated by national legislation for traditional dairy farms in both countries.