Submerged oscillating water columns (SOWC) are a type of hydraulic structures commonly classified as wave energy converters (WEC) that can extract energy from ocean surface waves in intermediate water depths. This study explores the effect of reducing the entrance loss and improving energy efficiency by modifying the SOWC opening. A basic SOWC device consists of two submerged cylinders with openings at the bottom that allow the flow to move in and out. A connecting pipe allows entrapped air to flow between the cylinders as waves pass. Ideally, cylinders are spaced at half a wavelength apart to maximize the height differential. A series of experimental tests have been carried out at Idaho State University’s Water Resources Lab to explore the validity of the concept. Numerical simulations using computational fluid dynamics (CFD) were completed and the efficiency of the SOWCs obtained. The results of 32 simulations using Stokes Cnoidal waves have been investigated for different wave configurations and SOWC cylinder openings. The effect of four parameters including the opening percentage and shape, water depth, wave height, and wave length were investigated. The numerical CFD modeling indicated that the entrance conditions and shape can affect the water elevation movement inside the chambers. Optimum openings can increase the efficiency by up to 15%.