Managed aquifer recharge (MAR) with recycled water or other alternative resources is one of the most rapidly growing techniques that is viewed as a necessity in water-short areas. In order to better control health and environmental effects of MAR, this paper presents two case studies demonstrating how to improve water quality, enable reliable tracing of injected water and better control and manage MAR operation in the case of indirect and direct aquifer recharge. Two water quality management strategies are illustrated on two full-scale case studies, including the results of the combination of non conventional and advanced technologies for water quality improvement, comprehensive sampling and monitoring programs including emerging pollutants, tracer studies using boron isotopes and integrative aquifer 3D GIS hydraulic and hydrodispersive modelling.