Integrated modeling of headwater watersheds in mountain environments is often limited by the lack of hydrological characterization and monitoring data. For the No-Name watershed in the Medicine Bow Mountains in Wyoming (USA), this research integrates regional surface and subsurface hydrological and geophysical measurements to create three-dimensional integrated hydrological models with which interactions between surface water, soil water, and groundwater are elucidated. Data used to build and calibrate the integrated model include a digital elevation model (DEM), stream discharge at the outlet of the watershed, soil-moisture data, weather data, and geophysical surveys including seismic refraction, airborne resistivity, and nuclear magnetic resonance (NMR). Based on interpretation of geophysical measurements, subsurface hydrostratigraphy consists of a top unconsolidated layer, a middle layer of fractured granite and metamorphic bedrock, and a lower protolith. Given that both measurements and interpretations have uncertainty, a sensitivity analysis was carried out to evaluate conceptual model uncertainty, which suggests the following: (1) for predicting stream discharge at the No-Name outlet, the most influential parameters are the Manning coefficient, DEM, hydrostratigraphy and hydraulic conductivity, and land cover. Compared to a lower-resolution DEM, a LiDAR DEM can lead to more accurate predictions of the stream discharge and stream elevation profile. (2) For predicting soil moisture, the most influential parameters are hydrostratigraphy and the associated hydraulic conductivities and porosities. (3) Based on a calibration exercise, the likely values for subsurface hydraulic conductivity at No-Name are ~10–5 m/s (the unconsolidated layer), ~10–6 m/s (fractured bedrock), and ~10–6 m/s or lower (protolith).