The Gulf of Thailand is ideal for studying eustatic sea level fluctuations in Southeast Asia due to its shallow basin and tectonic stability. However, our understanding of how this region’s relative sea level (RSL) has fluctuated over the Holocene epoch is far from complete. In this study, we used lithostratigraphy, loss on ignition, grain size, and pollen analyses to reconstruct the environmental changes in the Sam Roi Yot wetland, which was significantly influenced by seawater intrusion, driven by fluctuations in RSL in the Gulf of Thailand. Therefore, the analyzed pollen records of the sediment core from the wetland reflected variabilities in the RSL in the Gulf of Thailand. Subsequently, we found that after a sea level highstand prior to 4000 cal y BP, the RSL gradually fell with two significant regressions at c. 2950 and 1850–1450 cal y BP before rising at 1450–1050 cal y BP and declining after that. The inconsistency between RSL reconstruction based on our results and the global sea level changes simulated by the Glacial Isostatic Adjustment (GIA) model further suggests that long–term El Niño Southern Oscillations (ENSO) variabilities may have played a significant role in sea level changes in the Gulf of Thailand over the Late-Holocene period. Thus, during extended El Niño or La Niña conditions, the sea level would have been consistently lower or higher than expected from eustatic and isostatic processes alone. Overall, this study emphasizes the importance of considering regional factors such as ENSO to understand sea level changes in Southeast Asia.