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Abstract Understanding heavy metals in rivers is crucial, as their presence and distribution impact water quality, ecosystem health, and human well-being. This study examined the presence and levels of nine heavy metals (Cd, Cr, Cu, Fe, Hg, Mn, Ni, Pb, and Zn) in 16 surface water samples along the Chao Phraya River, identifying Fe, Mn, Zn, and Cr as predominant metals. Although average concentrations in both rainy and dry seasons generally adhered to WHO guidelines, Mn exceeded these limits yet remained within Thailand’s acceptable standards. Seasonal variations were observed in the Chao Phraya River, and Spearman’s correlation coefficient analysis established significant associations between season and concentrations of heavy metals. The water quality index (WQI) demonstrated varied water quality statuses at each sampling point along the Chao Phraya River, indicating poor conditions during the rainy season, further deteriorating to very poor conditions in the dry season. The hazard potential index (HPI) was employed to assess heavy metal contamination, revealing that during the dry season in the estuary area, the HPI value exceeded the critical threshold index, indicating the presence of heavy metal pollution in the water and unsuitable for consumption. Using the species sensitivity distribution model, an ecological risk assessment ranked the heavy metals’ HC5 values as Pb > Zn > Cr > Cu > Hg > Cd > Ni, identifying nickel as the most detrimental and lead as the least toxic. Despite Cr and Zn showing a moderate risk, and Cu and Ni posing a high risk to aquatic organisms, the main contributors to ecological risk were identified as Cu, Ni, and Zn, suggesting a significant potential ecological risk in the Chao Phraya River’s surface water. The results of this study provide fundamental insights that can direct future actions in preventing and managing heavy metal pollution in the river ecosystem.