The concentration and distribution of trace metals were determined in sediment cores from the Khuan Khi Sian wetland, Thailand. The sediment cores were collected from seven stations in the dry and wet seasons in 2022. The concentration of Pb, As, and Cd in the dry season were in the range 0.00–60.16, 0.00–6.68, and 0.00–0.92 mg/kg (dry weight), respectively. Meanwhile, the concentration of Pb, As, and Cd in the wet season were in the range 0.00–12.12, 0.00–3.86, and 0.00–0.92 mg/kg (dry weight), respectively. The vertical profiles of metal concentrations in core sediment show a general increase from bottom to top. Average concentrations of heavy metals in the sediments of the Khuan Khi Sian wetland are found to be lower than the sediment quality guideline. In the sediment cores, only As in the dry season exceeded the U.S. EPA standard. The calculated enrichment factor (EF) and the geoaccumulation index (Igeo) indicate that the sediments were moderately polluted with As in some locations. According to the Ri analysis, Pb was low risk but the criteria of ecological risk of As and Cd are considerable and they are considered high risk. This is potentially due to agricultural activities and land use around the wetland areas and municipalities. The concentration of As and Cd should be of concern and subject to regular monitoring.