Stream water enters and exits the streambed sediment due to hyporheic fluxes, which stem primarily from the interaction between surface water hydraulics and streambed morphology. These fluxes sustain a rich ecotone, whose habitat quality depends on their direction and magnitude. The spatio-temporal variability of hyporheic fluxes is not well understood over several temporal scales and consequently, we studied their spatial and temporal variation over a pool-riffle-pool sequence at multiple locations from winter to summer. We instrumented a poolriffle- pool sequence of Bear Valley Creek, an important salmonid spawning gravel-bed stream in central Idaho, with temperature monitoring probes recording at high temporal resolution (12- minute intervals). Using the thermal time series, weekly winter season seepage fluxes were calculated with a steady-state analytical solution and spring-summer fluxes with a new analytical solution that can also quantify the streambed thermal properties. Longitudinal pool-riffle-pool conceptualizations of downwelling and upwelling behavior were generally observed, except during the winter season when seepage fluxes tended towards downwelling conditions. Seepage fluxes near the edges of the channel were typically greater than fluxes near the center of the channel, and demonstrated greater seasonal variability. Results show that the interaction between streamflow and streambed topography has a primary control near the center of the channel whereas the interaction between stream water and groundwater table has a primary control on seepage fluxes near the banks of the stream.