The aim of this study is threefold: (1) to evaluate the effect of the physical properties of weathered granitic material (geometry and spatial distribution of hydraulic conductivity) on water fluxes at the outlets of two small and nearby agricultural catchments, Kerbernez and Kerrien (0.12 and 0.095 km 2), underlain by granite bedrock; (2) to explain the variations of nitrate concentration in streamwater in relation to the spatial distribution of dissolved nitrate in the groundwater; (3) to investigate the origin of the groundwater nitrate by analysing the reaction times of groundwater to variations of nitrate concentration in water recharge. These objectives were attained by developing a flow and nitrate transport model for the two catchments from geophysical measurements on the geometry and hydraulic conductivity of the weathered granite layer, and using data collected from soil surveys. The models were calibrated and validated from spatial and temporal observations of hydraulic heads and nitrate concentrations in groundwater and stream water. The flow models appeared to be less sensitive to the geometry of the weathered granite layer than the spatial distribution of hydraulic conductivity. Model results show that seasonal patterns of nitrate concentrations in streamwater result partly from the spatial distribution of nitrate concentration in the groundwater. The horizontal distribution of nitrate concentrations in groundwater derives from denitrification in the downslope domain. An analysis of the groundwater reaction times for both catchments shows that, following a variation in the recharge nitrate concentration; the time to reach equilibrium in the whole groundwater body is more than 14 years. In the Kerbernez catchment, the vertical distribution observed in groundwater nitrate concentrations appears to be caused by a temporal decrease of the nitrate concentration in the water recharge over the last 15 years.