We conducted hydrographic observations throughout the year to investigate seasonal variations of the hypoxic water mass distribution in the Upper Gulf of Thailand (UGoT). Hypoxic water masses were observed from June to November, with half of the UGoT occupied by hypoxic water in September. A hypoxic water mass appeared in the northeastern part of the UGoT in June and August, and moved westward over time. Low-salinity surface water moved from east to west as the rotational direction of surface circulation shifted with the reversal of monsoon winds. Westward movement of low-salinity water causes strong stratification in the northwestern part of the UGoT, leading to severe hypoxia. Numerical experiments showed high dissolved oxygen consumption rates around and offshore of river mouths, where hypoxic water is generated. This finding suggests that hypoxic water masses are transported to the south by physical processes. We examined how flooding affects hypoxic water mass formation. The volume of hypoxia in a flood year was approximately 2.5 times greater than in a normal year. In addition, hypoxia occurred in the dry season and extensive hypoxia was observed in the year after flooding. These results suggest that the hypoxic water mass persists for a long time after flooding.