The in-depth knowledge on management and reducing annual acidic pollution is important for improving the sustainable livelihood of people living in areas with acid sulphate soils (ASS). This study involved a long-term (2001–2006), large-scale canal water quality monitoring network (87 locations) and a field experiment at nine sites to quantify the dynamic variability of acidic pollution and its source in a coastal area with ASS in the Mekong River Delta of Vietnam. Widespread acidic pollution (pH <5) of surface water occurred at the beginning of the rainy season, while pH of the canal water remained high (7–8) at the end of the rainy season and during the dry season. The study identified canal embankment deposits, made of ASS spoils from canal dredging/excavation, as the main source of acidic pollution in the surrounding canal network. The findings suggested that there was a linkage between the amount of acidic loads into canal networks and the age of the embankment deposits. The most acute pollution (pH ~ 3) occurred in canals with sluggish tidal water flow, at 1–2 years after the deposition of excavated spoils onto the embankments in ASS. The amount of acidic loads transferred to the canal networks could be quantified from environmental parameters, including cumulative rainfall, soil type and age of embankment deposits. The study implied that dredging/excavation of canals in ASS areas must be carried out judiciously as these activities may increase the source of acidic pollution to the surrounding water bodies.