ABSTRACTThe aim of this study is to determine the level and source of pollution by potentially toxic elements (PTEs) due to torrential floods in the catchment area of the Drina River under complex geological conditions. The degree of soil and sediment pollution by PTEs was estimated by calculating the Pollution Index (PI) and the Geo‐accumulation index (Igeo). Sources of PTEs were determined using Principal component analysis (PCA) for soil and sediment and the Positive Matrix Factorisation (PMF) model for sediment. To fully include the spatial component when determining the source of PTEs, Bivariate Local Moran's I analysis was also applied. By comparing the applied methods, it was determined that PCA is suitable for determining the sources of PTEs in soil and for investigating the sedimentation process in sediment, while the PMF model is more suitable for determining the sources of PTEs in sediment. It was also determined that when the geological substrate is rich and after high‐intensity flooding, there is an increase in As, Cd, Co, Cu and Fe content in sediment compared with soil. Arsenic was partially impacted by anthropogenic factors, with Igeo values for soil (16.21%) and sediment (21.76%) at the polluted level.