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• Drip irrigation had a greater effect on surface heavy metals than flood irrigation. • Drip irrigation resulted in increased accumulation of heavy metals at 0–60 cm. • Heavy metals primarily accumulated at the centre between pipes. • Heavy metals accumulated at the wetting front edge following prolonged irrigation. • The Nemerow Index decreased with soil depth under both irrigation conditions. Different irrigation methods have variable effects on the physiochemical properties of soils. The predicted widespread replacement of flood irrigation with drip irrigation will alter the micro-environment of the associated soils in terms of migration, transformation, morphology, and toxicology of heavy metals and pesticides. The dynamics of heavy metals in soil under drip irrigation have only been investigated with regard to the use of sewage and reclaimed water; studies comparing these patterns across different irrigation methods are scarce. Here, we aimed to investigate the effects of drip and flood irrigation on heavy metal distribution in soil and the related risks in three typical agricultural systems in China. We used fixed-point sampling, digestion analytical methods, descriptive analyses, one-way analysis of variance (ANOVA), Nemerow pollution index analyses, and correlation analyses to investigate the different effects of drip and flood irrigation on heavy metals (Cd, Cr, Cu, Pb, and Zn) in soils from Hebei, Xinjiang, and Ningxia Provinces, China. Analyses of soil samples collected from drip-irrigated fields revealed significant differences in the concentrations of soil heavy metals at depths of 0–60 cm. Drip irrigation had a greater effect on heavy metal content in the soil surface than flood irrigation. In addition, heavy metals likely accumulated at the edges of the wetting fronts following prolonged irrigation. In comparison to drip irrigation, flood irrigation elevated pollution levels in the soil. The amount of fertiliser affected the leaching and migration of heavy metals in the soils by altering the physiochemical characteristics of the drip irrigation solution. Drip irrigation alters the dynamics of heavy metals in soil by influencing their migration and accumulation patterns. This effect can be attributed to the methods of adding water and fertilisers to the soil under drip irrigation. Altering these variables can impact the level of heavy metals that bioaccumulate in crops. This study provides a scientific basis for reducing heavy metal pollution under drip irrigation. [ABSTRACT FROM AUTHOR]