Although streambed dynamics are known to be complex and three-dimensional, flux within the subsurface is often estimated with simplified models for convenience, despite the errors this incurs. While three-dimensional (3D) models have the advantage of being able to capture complex flow paths within the subsurface, they are also more data intensive, requiring a detailed knowledge of both thermal and hydraulic streambed properties. Temperature data are relatively easy to acquire at a high resolution within a natural stream environment; however, it is typically more difficult to capture hydraulic head measurements at this same resolution, making it difficult to apply appropriate boundary conditions to 3D models in order to estimate streambed fluxes from heat tracer techniques alone. In this study, we examine the consequences of the lack of detailed head data for parameterizing boundary conditions. We tested the abilities of three 3D heat and water transport models with increasingly complex boundary conditions to match observed thermal patterns and predict streambed fluxes. All three models showed similar spatial patterns of high and low fluxes. The amplitude of predicted daily temperature variation at a depth of 0.25 m and 0.5 m below the streambed was generally within 0.1 °C (i.e. within sensor error) of observed, while all three models typically underestimated daily temperature variation in advective areas at a depth of 0.1 m. The results of this study suggest that 3D heat transport models of streambeds may be more limited by the low sensitivity of hydraulic conductivity to small temperature variations than by the lack of detailed hydraulic head data for parameterizing boundary conditions.