We investigated the response of hyporheic exchange flow (HEF) to wood removal in a small, low-gradient, gravel bed stream in southeast Alaska using a series of groundwater models built to simulate HEF for the initial conditions immediately after wood removal and 1 month, 2 years, 4 years, and 16 years following wood removal. The models were based on topographic surveys of the stream channel and surrounding floodplain, and surveyed water surface elevations (WSEs) were used to assign stream boundary conditions. Using the groundwater flow model, MODFLOW, and the particle tracking model, MODPATH, we calculated hyporheic exchange fluxes, their residence time distributions, and both longitudinal and plan view spatial patterns of downwelling and upwelling zones. In the first few years, streambed scour and sediment deposition smoothed the streambed and WSE profile, reducing HEF. Also, large contiguous patches of downwelling or upwelling were fragmented, nearly doubling the total number of patches present on the streambed. As the stream continued to adjust to the loss of wood, those trends began to reverse. Accretion of sediment onto alternating bars resulted in better developed pool-riffle morphology, enhanced HEF, and increased residence times and also resulted in downwelling and upwelling zones coalescing into elongated patches along bar margins. This study showed that the hyporheic zone is sensitive to changes in wood loading and that initial changes in HEF resulting from the direct effects of wood removal were contrary to longer-term channel adjustments to changes in wood loading.