In the semi-arid Brazilian Northeast, the development of alluvial aquifers exploitation during the last 10 years has increased water availability in dry season for irrigation and domestic supply of rural communities; however, water availability for all the categories of uses and users is an open question. In the Forquilha watershed (221 km²; 5°17' S, 39°30' W), the 23 km long and 250 m wide alluvial aquifer (2,3 hm3) is used for irrigation and domestic water supply. Alluvial aquifer dynamics is seasonal with recharge during rainy season and water table decreases during the dry season, accentuated by pumping. During the dry season, groundwater salinity increases from 0,2 up to 1,5 g/L imposing pumping restrictions. Water table and electric Conductivity (EC) monitoring, environmental isotope 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 to investigate the origin of salinity of alluvial groundwater and to evaluate long-term contribution of basement fractured-rock to the alluvial aquifer. The functioning hypotheses have been tested with 3D physical-based finite-element hydrological and transport modeling (Feflow®) on a section (1,5 km length) of the alluvial aquifer where exploitation is intense. 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. Intensive pumping of alluvial ground water for irrigated crops leads to higher recharge by low salinity water during flood events and, that way, to short-term decreases in EC. However, irrigation water evaporation in soils leads to salt accumulation in the unsaturated zone which can be