Population growth and agricultural intensification are ever more demanding in water resources, and threaten their quality and quantity, especially in semi-arid and arid areas. The Sahara desert is typical of these multiple constraints and rapid changes making sustainable management of water resources a major issue. The wide regional aquifers have nearly fossil water. In contrast, alluvial aquifers associated with small wadis are recharged nearly each year by the rare floods. In the case of Wadi Tamanrasset, in southern Algeria, the alluvial aquifer is exploited intensively because of its accessibility and its good chemical quality. The physical conditions commanding flow and recharge of groundwater, and especially the transfer from surface to groundwater, were studied by combining hydrodynamics and isotopic tracers (18O, 2H). Monthly monitoring of groundwater level in around thirty wells was complemented by automatic recorders with hourly time steps since March 2016 in three wells, along a 600 m transect perpendicular to the wadi bed. The slow response of the water table is visible only two months after the first flood; its maximum rise was 1 m in 2016. Isotopic analyses of rainwater on a daily time scale, of the wadi water on a 1 h time scale during runoff and of groundwater (two complete campaigns in the dry and wet seasons and a specific monitoring of the transect every month) have provided additional information on surface-groundwater transfer.