To develop predictive models for solute transport in the subsurface, the mechanisms governing transport must be understood and quantified. In this study, we used the HYDRUS-2D variably saturated flow and transport model to describe the observed mass flux breakthrough curves (BTCs) of three surface-applied tracers—Br−, Cl−, and pentafluorobenzoic acid (PFBA)—to a single well from which the tracers were pumped. Axisymmetrical transport simulations of the data indicated the presence of an active seepage face along the soil–well interface near the water table. The calculated cumulative water flux to the well through the seepage face was found to be 120% of the variable flux boundary into the well through the submerged zone. In addition, calculated mass fluxes of Br, Cl, and PFBA through the seepage interface were approximately 8, 4, and 11 times, respectively, those through the variable flux boundary. Calculations suggest that a seepage face may be responsible for causing the early arrival of the solutes and the overall shape of the BTCs. Our study indicates the potentially important role a seepage face along the soil–well interface may have in modeling water flow and chemical transport to wells in variably saturated, unconfined aquifers.