In this paper, a weighted discontinuous Galerkin finite element method and an upwind format are presented to solve the coupled Brinkman–Darcy flow and transport model. The flow in a highly permeable region of the model is governed by the Brinkman equations, and the percolation in the porous media is controlled by the Darcy equations, which are coupled by three interface conditions. The permeability coefficients in this model are strongly nonhomogeneous, anisotropic, and discontinuous; the transport equation is a convection-dominated problem; and the velocity field in the porous media domain does not satisfy the divergence-free condition. A weighted discontinuous Galerkin finite element method is used to solve the complex permeability coefficient problem and an upwind scheme is used to solve the convection dominated problem. The interface conditions can be naturally incorporated into the discrete formulation without introducing additional variables. Optimal error estimates are obtained for the semi-discretization and the full discretization with the backward Euler scheme in suitable energy norm. A series of numerical experiments are provided to illustrate the proposed method, including testing the convergence and accuracy of various types of meshes; simulating fluid flow in complex porous media such as obstacles, layered media, and curved interfaces; and studying the coupled flow behavior of surface-subsurface flows with contaminant transport.