In the semi-arid Brazilian Northeast, the development of small alluvial aquifers exploitation over the last 10 years has increased water availability for supply of rural communities. Nevertheless, an important constrain to some uses appears to be the salinity of the water. The purpose of this study was to analyze hydrological relationships between groundwater and surface water systems in a small semi-arid watershed with growing irrigation withdrawals. Water table and electric conductivity (EC) monitoring, and chemical analyses have been conducted from 09/2000 to 06/2007 in order to investigate the variations of observed EC in time and space and propose a functioning model. A mass-balance conceptual model has been set up and used in combination with geochemistry. EC within-year variations can be explained 1) by the main recharge mechanism of the aquifer by flood infiltration in river-bed, 2) by the local groundwater renewal rate which is related to hydraulic conductivity heterogeneity of the layers and 3) by the mass flux from basement aquifer. Water evaporation in soils leads to salt accumulation in the unsaturated zone which can be subsequently leached towards the saturated zone when extreme flood event occur, like for example the one observed in 2004.