In headwater catchment, the calibration of hydrological models is complex due to the scarcity of data in mountainous areas. Here, an innovative methodology is developed to condition hydrological model parameters by using magnetic resonance sounding (MRS) measurements in combination with stream flow rate data. MRS has the specificity in the various geophysical imaging techniques of being mainly sensitive to the vertical distribution of water content among the subsurface. In a way very similar to hydraulic head observations, these local distributions of water content may serve as information in a hydrological model to pattern subsurface flow by seeking model parameters. Simulations are run with different sets of parameters of a hydrological model. Each simulation provides as an output a 4-D map (3-D spatial plus time) of the vertical water content distributions over the whole catchment and their fluctuations over time. This output is then used to simulate the MRS signal that would be produced by the estimated water content. The simulated MRS signal is compared to measured MRS data to determine which hydrological simulations (which model parameters) are close to observations. The approach is applied on a hard-rock headwater catchment housing a very shallow and thin aquifer where an MRS survey covers the whole studied site. Hydraulic parameters of an integrated hydrological model of the catchment are spatially distributed by zones with uniform values, the prior delineation of the zones being guided by pedological studies. As MRS measurements supply local but spatially distributed information, the method conditions the various zones on their parameter values in a much better way than the classical (in headwater catchments) measure of the stream flow rate at the outlet of the system. Finally, hydrological simulation and time-dependent MRS forward calculations can help identifying possible locations for MRS stations to monitor the transient behavior of the hydrological state of the catchment.