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Groundwater–surface water interaction, particularly on exchange fluxes between streams and aquifers, plays a large role in the prerequisite conditions for the study of contaminants and nutrients in the hyporheic zone. One way to quantify these fluxes is by using heat as an environmental tracer. This study quantitatively analyzes the spatial heterogeneity and uncertainty of the vertical turbulent flow of a canopy in the Walker River Basin in Nevada, USA, using the thermal tracer method and the VFLUX software tool. Using the high spatial resolution temperature data measured by the US Geological Survey in the Walker River Basin in Nevada, with the finite element software, COMSOL Multiphysics, it establishes a two-dimensional, full-transect, water-thermal coupling calculation model for the river. The results show that long-term vertical hyporheic flux is between − 111.78 and 86.07 L/m2/d. The average vertical hyporheic flux under seasonal conditions was − 44.35 L/m2/d and − 36.78 L/m2/d in summer and winter, respectively, and the flux exhibits a non-monotonic change with increasing depth. By observing the similarity between the spatial distribution of streambed hyporheic exchange fluxes in winter and summer, as well as the distribution of the streambed profile temperature field, it was found that the spatial distribution of the average streambed hyporheic exchange fluxes can be clearly shown by the streambed profile temperature field in the corresponding season. [ABSTRACT FROM AUTHOR]