Deuterium, oxygen-18 and chloride were analyzed for 84 samples from deep and shallow wells, precipitation and the river White Nile to investigate groundwater recharge/discharge relations in the semi-arid central Sudan. Spatial and vertical variation in isotopic signature and chloride concentration in the groundwater show similar patterns and indicate local recharge and evaporative discharge. Progressive decrease in isotopic composition along the regional groundwater flow path demonstrates aquifer continuity down the NW–SE recharge-discharge path. Isotope-heavy recharged water progressively mixes with lighter older groundwater formed during cooler and humid conditions in the late Pleistocene. However, evaporative fractionation in the flow path’s final reach in the southeast re-enriches the isotopic composition and suggests evaporative loss of groundwater as the plausible discharge mechanism. Chloride concentration increases down the gradient from the recharge area and reaches its peak in the discharge zones indicating: lack of recharge from direct infiltration down the gradient, evaporation and prolonged rock/water interaction. Head differences and increased isotopic concentration in the vicinity of the White Nile suggest recharge from the river from subsurface flow. Reduced chloride content and relatively heavier isotopic composition in the deep groundwater beneath the wadi of Khor Abu Habil indicate recharge from the streambed into the deep aquifer.