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In this paper, we consider flow and transport problems in thin domains. The mathematical model considered in the paper is described by a system of equations for velocity, pressure, and concentration, where the flow is described by the Stokes equations and the transport is described by an unsteady convection-diffusion equation with non-homogeneous boundary conditions on walls (reactive boundaries). We start with the finite element approximation of the problem on unstructured grids and use it as a reference solution for two and three-dimensional model problems. Fine grid approximation resolves complex geometries on the grid level and leads to a large discrete system of equations that is computationally expensive to solve. To reduce the size of the discrete systems, we develop a multiscale model reduction technique, where we construct local multiscale basis functions to generate a lower-dimensional model on a coarse grid. The proposed multiscale model reduction is based on the Discontinuous Galerkin Generalized Multiscale Finite Element Method (DG-GMsGEM). In DG-GMsFEM for flow problems, we start with constructing the snapshot space for each interface between coarse grid cells to capture possible flows. For the reduction of the snapshot space size, we perform a dimension reduction via a solution of the local spectral problem and use eigenvectors corresponding to the smallest eigenvalues as multiscale basis functions for the approximation on the coarse grid. For the transport problem, we construct multiscale basis functions for each interface between coarse grid cells and present additional basis functions to capture non-homogeneous boundary conditions on walls. Finally, we will present some numerical simulations for three test geometries for two and three-dimensional problems to demonstrate the method's performance.