Wave and tide are important forcing factors that typically co-exist in coastal environments. A numerical study was conducted to investigate individual and combined effects of these forces on flow and mixing processes in a near-shore subterranean estuary. A hydrodynamic model based on the shallow water equations was used to simulate dynamic sea level oscillations driven by wave and tide. The oscillating sea levels determined the seaward boundary condition of the coastal aquifer, where variably-saturated, variable-density flow was modeled. The simulation results showed that waves induced an onshore upward tilt in the phase-averaged sea level (wave set-up). The resulting hydraulic gradient generated pore water circulations in the near-shore zone of the coastal aquifer, which led to formation of an upper saline plume (USP) similar to that due to tides. However, mixing of recirculating seawater in the USP with underlying fresh groundwater was less intensive under the high-frequency wave oscillations. In the case of combined forcing, wave-induced circulations coupled with the intra-tidal flows strengthened the averaged, circulating pore water flows in the near-shore zone over the tidal period. The circulating flows increased exchange between the subterranean estuary and ocean, contributing 61% of the total submarine groundwater discharge for the simulated condition in comparison with the 40% and 49% proportions caused by the same but separate tidal and wave forcing, respectively. The combined forces also created a more extensive USP with the freshwater discharge zone shifted further seaward. The freshwater flow paths in the intertidal subterranean estuary were altered with a significant increase of associated transit times. The interplay of wave and tide led to increased mixing between discharging fresh groundwater and recirculating seawater. These results demonstrated the complexity of near-shore groundwater systems and have implications for future investigations on the fate of land-sourced chemicals in the subterranean estuary prior to discharge to the ocean.