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Groundwater recharge studies in semi-arid areas are fundamental because groundwater is often the only water resource of importance. This paper describes the water balance method of groundwater recharge estimation in three different hydro-climatic environments in eastern Mediterranean, in northwest Greece (Aliakmonas basin/Koromilia basin), in Cyprus (Kouris basin and Larnaka area) and in Jordan (northern part of Jordan). For the Aliakmonas basin, groundwater recharge was calculated for different sub-catchments. For the Upper Aliakmonas basin (Koromilia basin), a watershed-distributed model was developed and recharge maps were generated on a daily basis. The mean annual recharge varied between 50 and 75 miWyear (mean annual rainfall 800 mm/year). In Cyprus, the mean groundwater recharge estimates yielded 70 mm/year in the Kouris basin. In the Larnaka area, groundwater recharge ranged from 30 mm/year (lowland) to 200 mm/year (mountains). In Jordan, the results indicated recharge rates ranging from 80 mm/year for very permeable karstified surfaces in the upper part of the Salt basin, where rainfall reaches 500 mm/year to less than 10 mm/year and to only about I mm/year in the southernmost part of the basin. For the north part of Jordan, a watershed-distributed model was developed and recharge maps were generated. This water balance model was used for groundwater recharge estimations in many regions with different climatic conditions and has provided reliable results. It has turned out to be an important tool for the managernent of the limited natural water resources, which require a detailed understanding of regional hydro(geo)logical processes. Copyright (C} 2007 John Wiley & Sons, Ltd.