The problem of solute transport in steady nonuniform flow created by a recharging and discharging well pair is investigated. Numerical difficulties encountered with the standard Galerkin formulations in Cartesian coordinates are illustrated. An improved finite element solution strategy is presented to overcome the numerical problem. The strategy is based on a formulation performed in three-dimensional curvilinear coordinates. This formulation is developed especially for the simulation of two-well injection-withdrawal tracer tests conducted in homogeneous or stratified aquifers. The formulation can also be applied to other types of problems involving transport in homogeneous and stratified aquifers. A three-dimensional finite element approximation is derived by two successive applications of upstream weighted-residual and subdomain collocation procedures.