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Industrial revolution induced contamination of lowland rivers and floodplain soils with heavy metals worldwide. This pollution was particularly significant in former coal mining regions where hard coal was utilised in various industrial facilities like coke, iron and steel works. The upper Odra River draining Ostrava Coal District in Czech and Upper Silesia mining region in Poland is an example of such a European river with strong historical pollution followed by modern one originating from heavy industry in times of communistic industrialisation in both countries. In the presented studies we sought 19th and 20th century transboundary contamination of the upper Odra River waters recorded in floodplain soil by the most common potentially toxic elements, i.e. lead and zinc as well as by the presence of magnetic particles (spherules). We expected to reveal the general pattern of the Odra River floodplain soil contamination with risk elements which allow us to differentiate sediments of the industrial and pre-industrial era. We used robust regression and robust principal component analysis, using a log-ratio methodology of compositional data analysis, which is a fast and effective tool in assessing contamination levels. Significant increases in risk element concentrations were found downstream from the Ostrava–Bohumin agglomeration, and in some places they exceed the safety limits for agricultural soils in Poland. A comparison of sediments within and outside of the inter-embankment zone showed no systematic difference in their contamination levels suggesting that the sediments were probably contaminated before dike construction mainly since the half of 19th century.