Agriculture is a major user of water resources and also contributes to water pollution from excess nutrients, pesticides and other pollutants. But the competition for water is increasing and the costs of water pollution can be high. Farming accounts for around 70% of water used in the world today. Climate change could affect water supply and agriculture through changes in the seasonal timing of rainfall and snow pack melt, as well as higher incidence and severity of floods and droughts. Sustainable management of water in agriculture is critical to increase agricultural production, ensure water can be shared with other users and maintain the environmental and social benefits of water systems. Agriculture needs therefore to use water in a more efficient way. Irrigation Management is important since it helps determine future Irrigation expectations. The goal of irrigation management is to use water in the most profitable way at sustainable production levels. For production agriculture this generally means supplementing precipitation with irrigation. The main challenge confronting water management in agriculture is to improve water use efficiency and its sustainability. This can be achieved through; an increase in crop water through irrigation, a decrease in water losses through soil evaporation that could otherwise be used by plants for their growth, and an increase in soil water storage within the plant rooting zone through better soil and water management practices at farm and area-wide (catchment) scales. Tracking and quantifying water fluxes at different spatial and temporal scales within the plant rooting zone remains a formidable challenge because of the interactions between water sources from rainfall, irrigation and subsurface water on plant uptake, soil evaporation, plant transpiration (water transpired by plants) and runoff or drainage losses from crop-growing areas. The use of isotopic and nuclear techniques to investigate the relative importance of soil and irrigation management factors that influence these interactions will greatly assist in the development of water management packages that involve the consideration of soil nutrient status, type of crops grown, growth stages and the overall agro-ecosystems to minimize not only water but also nutrient losses from the farmlands and enhance water and nutrient use efficiencies in agro-ecosystems under both rainfed and irrigated conditions.