Diffusive bottom boundary layers can produce upslope flows in a stratified fluid. Accumulating observations suggest that these boundary layers may drive upwelling and mixing in mid-ocean ridge flank canyons. However, most studies of diffusive bottom boundary layers to date have concentrated on constant bottom slopes. We present a study of how diffusive boundary layers interact with various idealized topography, such as changes in bottom slope, slopes with corrugations and isolated sills. We use linear theory and numerical simulations in the regional ocean modeling system (ROMS) model to show changes in bottom slope can cause convergences and divergences within the boundary layer, in turn causing fluid exchanges that reach far into the overlying fluid and alter stratification far from the bottom. We also identify several different regimes of boundary-layer behaviour for topography with oceanographically relevant size and shape, including reversing flows and overflows, and we develop a simple theory that predicts the regime boundaries, including what topographies will generate overflows. As observations also suggest there may be overflows in deep canyons where the flow passes over isolated bumps and sills, this parameter range may be particularly significant for understanding the role of boundary layers in the deep ocean.