As within many European rivers in mountainous areas, the Bienne River (Jura Mountains, France) has been severely impacted by the implementation of obstacles to river flow. The aim of this study is to better understand how hydro-sedimentary dysfunctions (complex alterations of sediment transport in response to river engineering) can influence contaminants storage along the river. The sediment pollution trajectory was reconstructed based (1) on a well-dated sediment core, and (2) on several sediment samples taken at different depths on six riverbank profiles. Age control was established with a well-defined 137Cs profile and time-related grain size transitions in the sediment core, and only relatively for riverbank profiles using a plasticizer and PCB contents as chemical markers of the Anthropocene. Riverbanks and the core are composed of fine-grained legacy sediments deposited during the 20th century. They covered the former active channel mostly composed of pebbles and cobbles. Historical contaminants were the highest in the most upstream station and declined in the downstream direction to reach relatively low values in the lower river section. This historical upstream signal poorly influences the geochemical composition of sediments in the lower reaches, due its attenuation by numerous human-made obstacles to river flow and to the limited sediment transport capacity of the river. According to an unmixing model, the contribution of the upper sediments only weights a small percentage of the sedimentary mixture at the river outlet. These results highlight the sedimentary storage capacity of historical contaminants in mountain coarse-bedded river. This phenomenon has been led by a riverbed narrowing and stabilization caused by deep alterations of hydro-sedimentary processes. It finally emphasizes storage of sedimentary contaminants and leads to limited source influences. Hence, this study shows the key role of sedimentary transport, which triggers spatial and temporal variability of contaminants stored in sediments.