Topography is a key control on runoff generation, as topographic slope affects hydraulic gradients and curvature affects water flow paths. At the same time, runoff generation shapes topography through erosion, which affects landscape morphology over long timescales. Previous modeling efforts suggest that subsurface hydrological properties, relative to climate, are key mediators of this relationship. Specifically, when subsurface transmissivity and water storage capacity are low, (1) saturated areas and storm runoff should be larger and more variable, and (2) hillslopes shorter and with less relief, assuming other geomorphic factors are held constant. While these patterns appear in simulations, it remains uncertain whether subsurface properties can exert such a strong control on emergent properties in the field. We compared emergent hydrological function and topography in two watersheds that have very similar climatic and geologic history, but very different subsurface properties due to contrasting bedrock lithology. We found that hillslopes were systematically shorter and saturated areas more dynamic at the site with lower transmissivity. To confirm that these differences were due to subsurface hydrology rather than differences in geomorphic process rates, we estimated all parameters of a coupled groundwater-landscape evolution model without calibration. We showed that the difference in subsurface properties has a profound effect on topography and hydrological function that cannot be explained by differences in geomorphic process rates alone. The comparison to field data also exposed model limitations, which we discuss in the context of future efforts to understand the role of hydrology in the long-term evolution of Earth’s critical zone.