Groundwater-surface water interactions in rivers are a critically important factor for fish spawning, as streamwater downwelling or upwelling of low-oxygen groundwater can affect egg survival. Assessing such dynamics at the reach scale using distributed temperature measurements as a tracer proved reliable in determining flux rates and directions in the hyporheic zone in a number of studies. Here, we report heat-based vertical flux rates from a heterogeneous gravel-bed stream reach used by spawning Atlantic salmon in the Scottish Highlands. Results showed mostly small downwelling fluxes (~0.3 m d−1), which were largely independent of discharge. Contrasting, and at times unusual flux-depth profiles (e.g., increasing flux with depth) were detected, consistent with the heterogeneous streambed material causing diverse hyporheic flow paths. This was tested in a numerical 2-D model setup attempting to reproduce such behavior with variable random hydraulic conductivity (K) fields. The 2-D model clearly demonstrated that strong deviations from the expected decrease of fluxes with depth can be explained by high heterogeneity coupled with relatively low K fields. This showed that using simple 1-D heat-based flux estimates in combination with 2-D models is a useful approach to testing hypotheses about the influence of variable streambed materials on groundwater–surface water exchange in an ecological context.