Southwestern Madagascar is a semi-arid region and a hot-spot of global change. On the Mahafaly plateau, people live with quasi-permanent water stress and groundwater, the only available resource, is difficult to exploit due to a complex hydrogeological environment. A methodology (suitable for humanitarian projects; <40kEuro) was developed in four phases to assess the sustainable exploitation of the water resource: (A) regional scale exploration, (B) village scale exploration, (C) drilling campaign, and (D) hydro-climatic monitoring. This integrated hydrogeophysical approach involves geophysical measurements (262 TEM-fast soundings, 2588 Slingram measurements, 35 electrical soundings), hydrochemical analyses (112 samples), and a piezometric survey (127 measurements). Two groundwater resources were identified, one deep (below 150m) and one shallow (<20m). Hydrochemical results highlighted the vulnerability of both resources: anthropic contamination for the shallower and seawater intrusion for the deeper. Therefore, subsequent geophysical surveys supported the siting of six boreholes and three wells in the shallow aquifer. This methodological approach was successful in this complex geological setting and requires testing at other sites in and outside Madagascar. The study demonstrates that geophysical results should be used in addition to drilling campaigns and to help monitor the water resource. In fact, to prevent over-exploitation, piezometric and meteorological sensors were installed to monitor the water resource. This unique hydro-climatic observatory may help (1) non-governmental organization and local institutions prevent future water shortages and (2) scientists to understand better how global change will affect this region of the world.