The simulation of preferential flow in structured soil using dual-porosity models requires separate sets of the hydraulic, transport, and mass transfer parameters and of the boundary conditions. Analyses of tracer experiments with two-domain models are limited by constraints in specifying separate boundary conditions (BCs) for each pore domain. The appropriate boundary conditions for dual-permeability models have not been systematically studied or addressed in experiments. The objective of this study was to numerically evaluate the effects on Br leaching from a tile-drained field of different surface boundary conditions for a two-dimensional dual-permeability model. For the previously described Br tracer experiment at the Bokhorst site (Germany), effects of irrigation intensities, flux- and resident-type solute BCs, and Br application domain on drain discharge and Br effluent concentrations were compared. The two-dimensional dual-permeability numerical model divides the soil into soil matrix (SM) and preferential flow (PF) domains. In case of ponding at the surface of the SM domain, water is redistributed toward the PF domain surface. The combination of detailed irrigation record, flux-type solute BCs, and solute application to the PF domain resulted in the largest Br leaching. In contrast, the lowest Br leaching was predicted for averaged irrigation rates, flux-type solute BCs and Br addition to the SM domain. For flux-type (third-type) solute BC application to both pore domains, enhanced Br leaching was obtained due to surface redistribution effects. Detailed irrigation patterns with realistic intensities predicted higher Br leaching than averaged intensities. In addition to surface effects, the temporal availability of Br in the preferential pathways seemed to control Br leaching patterns. The results suggest that the formulation of the upper BCs strongly affects two-dimensional dual-permeability Br leaching predictions. Proper experimental consideration of domain-specific BCs may help improve descriptions of preferential flow.