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The mechanisms and the rate of groundwater recharge were assessed for the uppermost aquifer used for water supply by local settlements in the area surrounding Timbuktu, Republic of Mali, using chloride budgets. The area receives a mean rainfall of 225mm annually. Three clusters of wells and three soil water profiles were sampled for the study. The well cluster in the vicinity of the River Niger showed effects of induced infiltration via an active wetland fed by the old canal, which once connected Timbuktu with the River Niger. For the well clusters further away from the river, an annual mean recharge of 4mm was found. A similar recharge, 1-2% of the precipitation, was found by assessing the recharge from the soil water chloride in three pits dug to 2.2-m depth. The recharge occurs preferably in depressions between dunes and due to channeling by soil crusts on the slopes of the dunes. This runoff-runon regime is probably the mechanism that allows any recharge to occur at all. The depressions, called mares in French, have standing water for extended periods after the rainy season, which is mirrored by gley patches in the subsoil. Occasional high nitrate concentrations in soil profiles indicate that conditions for nitrification and nitrate leaching occur after long drought periods followed by onset of heavy rain. This is a witness of the large variability of the precipitation climate in time and space, also mirrored in the variations of the figures for groundwater recharge. The moist conditions give growth to cyano-bacteria found on the soil surface in the mares. N-fixation by cyano-bacteria is probably the reason for occasional very high nitrate contents in soil and groundwater. The water demand by the local settlements has been assessed by using figures for population and livestock density and their water use. The water demand by the local population and their herds is sustainable in relation to the groundwater recharge assessed by this study.