Characterization of groundwater-surface water exchange is essential for improving understanding of contaminant transport between aquifers and rivers. Fiber-optic distributed temperature sensing (FODTS) provides rich spatiotemporal datasets for quantitative and qualitative analysis of groundwater-surface water exchange. We demonstrate how time-frequency analysis of FODTS and synchronous river stage time series from the Columbia River adjacent to the Hanford 300-Area, Richland, Washington, provides spatial information on the strength of stage-driven exchange of uranium contaminated groundwater in response to subsurface heterogeneity. Although used in previous studies, the stage-temperature correlation coefficient proved an unreliable indicator of the stage-driven forcing on groundwater discharge in the presence of other factors influencing river water temperature. In contrast, S-transform analysis of the stage and FODTS data definitively identifies the spatial distribution of discharge zones and provided information on the dominant forcing periods (≥2 d) of the complex dam operations driving stage fluctuations and hence groundwater-surface water exchange at the 300-Area.