Agriculture is one of the largest users of water resources and, at the same time, a considerable source of pollution of soils, atmosphere, surface water and groundwater. Water resources are used for water supply of rural settlements, cattlebreeding complexes and poultry plants, irrigation of pastures, meadows, lands as well as for power generation, pisciculture and recreation. Within the system of water use, the water quality has an influence on the health, ability to work and length of human life, vitality and productivity of agricultural animals, soundness of agricultural produce, efficient operation of structures, machines and mechanisms. Within the system of water disposal, wastewater, escape and drainage water as well as surface runoff containing salts, nitrite and ammonium nitrogen, phosphorus, pesticides, heavy metals, oil products and other pollutants enter aquatic ecosystems, change physical and organoleptic properties of water, chemical composition and biochemical regime of water bodies, structure of microorganisms and bioproductivity. Environmentally sound and economically efficient functioning of the systems of water use in agriculture is significantly dependent on the technical condition and reliability of operation of water-use systems, the volume and quality of used water. In compliance with above stated, the following priority problems have been revealed in agriculture: environmental (including medicobiological and veterinaryhygiene), economic, social, and technological. Systems analysis of a complex of problems of water use in agriculture has permitted the author to work out a concept of water use in agriculture and environmental auditing of water management activities, to develop environmental restrictions and requirements to water management activities, an integrated system of quality rating of used and disposed water, biotechnology of water quality improvement as well as environmental and technological fundamental principles of recycling systems of water use in agriculture.