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Managed Aquifer Recharge (MAR) is a promising method of increasing water availability in water stressed areas by subsurface infiltration and storage, to overcome periods of drought, and to stabilize or even reverse salinization of coastal aquifers. Moreover, MAR could be a key technique in making alternative water resources available, such as reuse of communal effluents for agriculture, industry and even indirect potable reuse. As exemplified by the papers in this Special Issue, consideration of water quality plays a major role in developing the full potential for MAR application, ranging from the improvement of water quality to operational issues (e.g., well clogging) or sustainability concerns (e.g., infiltration of treated waste water). With the application of MAR expanding into a wider range of conditions, from deserts to urban and coastal areas, and purposes, from large scale strategic storage of desalinated water and the reuse of waste water, the importance of these considerations are on the rise. Addressing these appropriately will contribute to a greater understanding, operational reliability and acceptance of MAR applications, and lead to a range of engineered MAR systems that help increase their effectiveness to help secure the availability of water at the desired quality for the future.