Land surface models (LSMs) used in climate modeling include detailed above-ground biophysics but usually lack a good representation of runoff. Both processes are closely linked through soil moisture. Soil moisture however has a high spatial variability that is unresolved at climate model grid scales. Physically based vertical and horizontal aggregation methods exist to account for this scaling problem. Effects of scaling and aggregation have been evaluated in this study by performing catchment-scale LSM simulations for the Rhône catchment. It is found that evapotranspiration is not sensitive to soil moisture over the Rhône but it largely controls total runoff as a residual of the terrestrial water balance. Runoff magnitude is better simulated when the vertical soil moisture fluxes are resolved at a finer vertical resolution. The use of subgrid-scale topography significantly improves both the timing of runoff on the daily time scale (response to rainfall events) and the magnitude of summer baseflow (from seasonal groundwater recharge). Explicitly accounting for soil moisture as a subgrid-scale process in LSMs allows one to better resolve the seasonal course of the terrestrial water storage and makes runoff insensitive to the used grid scale. However, scale dependency of runoff to above-ground hydrology cannot be ignored: snowmelt runoff from the Alpine part of the Rhône is sensitive to the spatial resolution of the snow scheme, and autumnal runoff from the Mediterranean part of the Rhône is sensitive to the spatial resolution of precipitation.