Predicting and managing water resources at regional scale under different climate and socio-economic scenarios is crucial to support drinking water supply and other sectors. At the same time, protecting rivers and wetlands from pollutions and droughts is essential and must include groundwater given its contribution to surface water. Yet, assessing temporal and spatial variability of groundwater contributions to surface water is constrained due to limited observations. This study aims to quantify the spatio-temporal distribution of groundwater discharge (hereafter called “GW discharge”) zones, i.e. the groundwater flow to rivers and wetlands, estimated by calibrated regional groundwater flow models (French AquiFR platform). We compare simulation results with two types of surface observations: (i) the spatial distribution of surface water (BD TOPO, RAMSAR and Natura 2000 database) and (ii) an innovative datasets, the river intermittence observed in headwaters (ONDE network). Results show that simulated GW discharge zones are consistent with the observed location of rivers and wetlands. Time variations in GW discharge are well correlated with the intermittence observed at 396 of the 515 selected stations. Of these, groundwater model continues to feed surface water upstream of the station for ∼75 % of observed river drying up events, which may be consistent with a small alluvial flow. The groundwater withdrawals are shown to have a strong impact on the GW discharge and thus on the river intermittence.