Water column conditions in the Gulf of Thailand (GoT) were analyzed by considering four major factors including surface heat fluxes, freshwater inputs from river discharge and atmospheric fluxes, tidal and wind stirrings. The analytical results suggested that surface heat fluxes and tidal stirring are the most important factors to control water column conditions, followed by freshwater fluxes. Well-mixing was predicted to occur from November to February resulted from relatively large tidal stirring, surface heat loss and low freshwater input, but the climatological density data suggested stratification during this period because of local freshwater accumulation. The South China Sea (SCS) and the northeast wind played significant contributions to freshwater accumulation by generating surface water flow into the gulf during the northeast monsoon. On the other hand, the development of stable and strong stratification during the southwest monsoon was enhanced by SCS subsurface water intrusion and surface outflow induced by the southwest wind. Strong surface heat fluxes coincident with SCS intrusion in April and May make water stratification more complex. This phenomenon generates double thermocline and multi-stratified water in some GoT area.