The effect of reducing submergence depth at a low and moderate Reynolds number flow is investigated using large eddy simulation (LES) around a matrix of cubes. The submerged body is modeled using an immersed boundary method, while the free-surface is accounted for using a moving mesh. Results show that for reducing the submergence depth, the forces acting on the cube reduce as the force variation increased. Variation in depth is also found to influence the level of damping and redistribution of turbulence near the free-surface boundary. Both submergence depth and Reynolds number are also found to influence the dominant free-surface signature and shedding frequencies from the cube. In the interobstacle region (IOR), the variation of Reynolds number and submergence depth is found to have little effect.