Hyporheic exchange, enhanced by complex stream channel morphology, can influence biogeochemical processing in the streambed. These processes chemically alter water passing temporarily through the streambed, which eventually returns to the stream channel and can potentially affect surface water quality. To assess the degree of biogeochemical cycling induced by complex streambed morphology, we instrumented two 20-m reaches of Red Canyon Creek, Wyoming, each containing a small log dam, with in-stream minipiezometers and temperature data loggers. We simultaneously observed pore water geochemistry and streambed temperature dynamics in several bedforms located upstream or downstream of the dams. We modeled seepage flux into the streambed using heat transport modeling. Upstream of the dams, low-permeability sediments have settled out in low-velocity pools, and enhanced anaerobic biogeochemical cycling occurred in the streambed. Rapid flux into the streambed occurred in glides immediately above the dams, where streambed temperature dynamics and geochemistry were nearly identical to the stream. In riffle sequences downstream of the dams, the streambed was oxygen rich, showed evidence of nitrification, and temperature dynamics indicated high connectivity between the streambed and the stream. Further downstream, streambed pore water geochemistry indicated ground water discharge occurring at the pool-riffle transition. Assessing streambed biogeochemical cycling may be facilitated by coupling streambed temperature measurements with pore water geochemistry and can aid in understanding how hyporheic exchange contributes to overall stream biogeochemistry.