The Ohře River has received contamination from metal mining and metallurgy (mainly Cu, Pb, Sn, U, Zn) over the previous five centuries. This contamination history has been poorly documented. Contamination has entered the river system in its middle reach, where the channel is incised and bedrock confined, which impedes overbank deposition. Our objective was to locate and describe a sedimentary record in this unfavourable depositional setting. Three former channel bars that have coalesced with the riverbank were revealed by examination of historical and current maps and a digital terrain model. Manual coring in the bar and in situ (handheld) X-ray fluorescence (XRF) spectroscopy provided data for developing a contamination chemostratigraphy, which was correlated with the mining history in the region. Detailed topographic examination of the bar and valley edge was important to understanding the evolution of one of the bars. Optically stimulated luminescence (OSL) dating was used to verify the timing of deposition. Handheld XRF for in situ analysis of element composition is efficient for studying contaminated sediment bodies with complex stratigraphy, which require extensive coring and stratigraphic correlation. Despite the unfavourable settings, the channel bars trapped sufficient sediment to produce a record that correlates with the history of contamination in the drainage basin. In the bar studied in greatest detail, we observed a surprising amount of contamination passing through the Ohře River channel (up to 300 mg kg−1 of Cu, 340 mg kg−1 of Pb and 630 mg kg−1 of Sn in fine sand and silt deposits) associated with a pollution climax in the sixteenth and seventeenth centuries. Modern contamination (Hg and U deposited in the nineteenth and twentieth centuries) was entrapped with low efficiency based on comparable concentrations of Hg and U located 90 km downstream. The efficacy of the use of historical maps and detailed fieldwork was demonstrated by identification of unique depositional meso-environments, which are rare in bedrock-confined fluvial systems. The contamination chemostratigraphy of the bar deposits was correlated with the local mining and pollution history and contributed to an understanding of the bar evolution. The approach used in our study may be applicable to other montane rivers with historic ore mining and processing in their basins.