In the Sahel region, temporary rivers and ponds constitute green spaces of welfare where sustainable development requires parsimonious management of water resources. The Komadugu Yobe valley in Eastern Niger is presented here as an example case of recent agricultural development based on irrigated pepper cropping. Piezometric maps indicate there that the river recharges the upper Quaternary aquifer. A simplified numerical model allows to quantify the exchanges between the river and the aquifer, based mainly on exploration geophysics data and three piezometric records, covering between 1 and 3 years of our 4 years modeling period. Recharge at the valley axis is modeled with a linear river coefficient constant for each hydrological year. The main findings are that: (i) during dry years, the river is disconnected from the aquifer and separated from it by a layer of unsaturated medium, (ii) however, this effect can be reversed, such as during the 2010–2011 wet year or after the Sahelian drought event of the 1980s and 1990s, (iii) the infiltration rate from the river amounts to 30–40 % of its total discharge and to at least four times the abstraction for pepper irrigation along its 150 km lower course at the Niger–Nigeria boundary, which implies that neither the aquifer recharge nor the river discharge is at risk due to the present agricultural development. Similar modeling near temporary river axes could provide some help in water resource management in the Sahel.