A 2-D Lattice Boltzmann Method (LBM) coupled with a Sub-Grid Stress (SGS) model is proposed and validated by flows around a non-submerged spur dike in a channel. And then the LBM-SGS model is further applied to flows in a pumping-station forebay. Shallow water equations are numerically solved by the LBM and the turbulence can be taken into account and modeled efficiently by the Large Eddy Simulation (LES) model. The bounce-back scheme of the non-equilibrium part of the distribution function is used at the inlet boundary, the normal gradient of the distribution function is set as zero at the outlet boundary and the bounce-back scheme is applied to the solid wall to ensure non-slip boundary conditions. Firstly, the model successfully predicts the flow characteristics around a spur dike, such as circulating flow, velocity and water depth distributions. The results are verified by the experimental data and compared to the results obtained by conventional Smagoringsky Model (SM) of LES. Finally, the LBM-SGS model is used to further predict the flow characteristics in a forebay, such as secondary flow and water level. The comparisons show that the model scheme has the capacity to simulate complex flows in shallow water with reasonable accuracy and reliability.