Groundwater recharge is an important, yet often a highly uncertain upper boundary condition in groundwater flow models for fractured rock. The net infiltration at ground surface can often be estimated from water budgets, but the redistribution of water between a soil layer and the underlying bedrock is much more difficult to quantify. To address this question, we studied the role of lateral flow diversion at the soil–rock interface and how it influences the percentage of net infiltration that becomes inflow into the bedrock. Numerical experiments were performed with different net infiltration conditions, soil–rock hydraulic conductivity contrasts, hydraulic gradients, and most notably, rock heterogeneity. The rock was first represented as a deterministic homogeneous continuum, then as a stochastic heterogeneous continuum and analyzed with Monte Carlo simulations. The heterogeneous simulations predicted a large variation in the inflow into the rock between different stochastic realizations (from 50 to 100% of the net infiltration). Furthermore, at high hydraulic gradients in the bedrock, the mean flux into the rock from the heterogeneous simulations was smaller than the corresponding results from the homogeneous medium. The heterogeneous simulations showed formation of local unsaturated zones below the groundwater table. These occurred in cases with large hydraulic gradients at locations with large hydraulic conductivity contrasts, with low-conductive regions overlying high-conductive ones. This phenomenon was not captured with the homogenous models, which thereby may overestimate flux into fractured rock in cases where hydraulic gradients are large.