The current study was conducted to (1) examine seasonal and spatial distribution of heavy metals and metalloid in sediment from the Saigon River and (2) apportion and quantify their pollution sources. Ninety-six sediment samples were taken in the rainy and dry season on 13 sampling sites, distributed over the lower reaches of the River, to analyze for exchangeable concentration of 11 heavy metals and metalloid (Al, B, Cd, Co, Fe, In, Mn, Ni, Pb, Sr, and Zn), pH, EC, organic carbon content, and particle-size distribution. Generally, the concentration of 11 elements was ranked in the order Mn > Al > Fe > Zn > Sr > In > B > Ni > Co > Pb > Cd. Hierarchical cluster analysis grouped 13 sampling sites into two parts based on the similar concentration of the 11 elements. Three-way analysis of variance showed that the total exchangeable concentration of 11 elements was significantly higher in the rainy season than in the dry season and in the upper part than in the lower part of the river. Principal component analysis/factor analysis and correlation analysis revealed that three pollution sources (PS) may contribute to enriching the 11 examined elements in the sediment. These sources included (PS1) from catchment through water erosion over natural areas, explaining 83%, (PS2) mixed sources from catchment through water erosion over agricultural fields and inside Ho Chi Minh City, accounting for 6%, and (PS3) mixed sources from lowland areas, explaining 7.8% of the total variance of the elements. In brief, the sediment concentration of 11 metals and metalloid varied with season and space and three major pollution sources from river catchment, inside Ho Chi Minh City, and lowland contributively enriched the elements in the sediment of the River. Display omitted •Sediment can serve as a sink/source of heavy metals (HM) for aquatic ecosystems.•11-HM concentrations in sediment from the Saigon River varied with season and space.•Rainy season had significantly higher concentration of 11 HMs than the dry season.•River catchment, inside Ho Chi Minh City, and lowland were major sources of 11 HMs.