Degraded soils in the sub-Saharan zone are often unproductive because of nutrient imbalance and an inadequate water supply. We conducted an experiment in the northern sudanian climate zone of Burkina to study the effect of integrated local water and nutrient management practices on soil water balance, sorghum performance and sorghum’s water use efficiency. The trial (Ferric Lixisol, 1.5% slope) consisted of two replications of nine treatments in which soil and water conservation (SWC) measures (stone rows, grass strips) and organic or mineral N-inputs (compost, manure, urea-N) were applied alone or in combination and compared to a control treatment with no N-input and no SWC measure. Application of compost improved soil water storage in the sorghum-rooting zone (0–80 cm) most when combined with stone rows or grass strips and when the year had well-distributed rainfall. However, during an erratic rainy season there was less soil water storage in the organic treatments than in the mineral treatment. Supplying compost increased evapotranspiration and soil drainage more than nutrient inputs did. Furthermore, stone rows allowed greater evapotranspiration and drainage than grass strips, and the two permeable barriers alone had a significant effect on soil water storage compared with treatments without barriers. In the rain-fed cropping system studied, we found that in an erratic rainy season with frequent periods of water stress, the stone rows or grass strips combined with compost reduced runoff and increased soil water storage and sorghum biomass production. These combined practices created sound soil water conditions and were able to satisfy the sorghum’s water demand for growth. We conclude that the synergistic effect of water-harvesting practices and the supply of organic or mineral resources increased water use efficiency. It seems that an optimum combination of organic resources and fertilisers could improve the water use efficiency (i.e. reduce runoff and drainage losses) and the productivity of Sahelian rain-fed agriculture.