A conceptual model of hydrostratigraphic and structural influences on 3D streamflow generation processes is tested in the Whiskey Creek watershed located in the Chuska Mountains of the Navajo Nation along the northern NM/AZ border. The role of hydrostratigraphy and structure in groundwater processes has been well studied. However, influences of heterogeneity due to geologic structure and stratigraphy of mountain blocks on 3D streamflow generation has received less attention. Three-dimensional flow in mountainous watersheds, such as Saguache Creek (CO) and Rio Hondo (NM), contributes significant amounts of groundwater from deep circulation to streamflow. This fully 3D conceptual model is fundamentally different than watersheds characterized as 2D, those dominated by surface and shallow subsurface runoff, because 3D watersheds can have much longer flowpaths and mean residence times (up to 1000s of years). In contrast to Saguache Creek (volcanic bedrock) and Rio Hondo (crystalline metamorphic), the bedrock geology of the watersheds draining the Chuska Mountains is primarily comprised of sedimentary bedrock capped by extrusive volcanics. We test this conceptual model using a combination of stream gauging, tritium analyses, and endmember mixing analysis (EMMA) on the general ion chemistry and stable isotope composition of water samples collected in 2013-2016. Springs that emerge from the Chuska Sandstone are tritium dead indicative of a large component of pre-bomb pulse water in discharge and deeper 3D flow. EMMA indicates that most streamflow is generated from groundwater emerging from the Chuska Sandstone. Gaining/losing conditions in Whiskey Creek are strongly related to hydrostratigraphy as evidenced by a transition from gaining conditions largely found in the Chuska Sandstone to losing conditions where the underlying Chinle Formation outcrops. Although tritium in Whiskey Creek suggests 3D interactions are present, hydrostratigraphic and structural controls may limit the occurrence of longer residence times and longer flow paths. Mountainous watersheds similar to the 3D hydrostratigraphic and structurally controlled models will exhibit different responses to perturbations, such as climate change, than watersheds that fit existing 2D and 3D conceptual models.