The Gulfs of Patras and Corinth, located in central western Greece, bordering with the Ionian Sea to the east and the Corinth Canal to west, are examined as a unified system. This semi-enclosed hydrodynamic system is divided by the Rio–Antirio strait, which is a microtidal environment. Based on 3D simulations using MIKE 3 FM (HD), the combined action of wind- and tide-induced flow was studied in the whole basin of the system. At the open boundaries, tidal astronomical constituents were used as boundary conditions, and steady light winds of 4 m/s for all the directions of the wind were considered. The action of the tide under the effect of wind generates a characteristic structure of the flow. Cyclonic and anticyclonic eddies form in the Gulf of Patras and in Nafpaktos Bay, during the ebb tide and under the SW wind; meanwhile, as strong wind-induced currents form near the shore, according to the direction of the wind, and the tidal flow moves from the east to the west of the system. The remaining part of the Gulf of Corinth remains nearly unaffected. The action of the NE wind and the flood tide form a similar flow structure, although the structure of the eddies is altered. Moreover, comparing the exchange flow rate between the gulfs for N, NE, and NW winds with the purely tidal flow, it has been shown that all these winds oppose the exchange flow rate, while S, SE, and SW winds favor the exchange flow rate at the strait. Our study of this system reveals that the Gulf of Patras and the western area of the Gulf of Corinth are mostly affected by the combined action of wind and tide, leaving the central part of the Gulf of Corinth unaffected. The wind action also affects flow characteristics between the gulfs, by opposing or favoring the exchange flow rate at the Rio–Antirio strait.