To understand the long-term fate of fish assemblages in the context of global change and to design efficient restoration measures in river management, it is essential to consider the historical component of these ecosystems. The human-impacted Seine River Basin is a relevant case that has experienced the extinction of diadromous fishes over the last two centuries and has recently witnessed the recolonization of some species. One key issue is to understand the historical evolution of habitat accessibility for these migratory species. Thanks to the unique availability of historical, mainly hand-written sources of multiple types (river engineering projects, navigation maps, paper-based databases on oxygen, etc.), we documented and integrated, in a geographic information system-based database, the changes to physical and chemical barriers in the Seine River from the sea to Paris for three time periods (1900s, 1970s, and 2010s). The potential impact of these changes on the runs of three migratory species that have different migratory behaviors—Atlantic salmon, allis shad, and sea lamprey—was evaluated by ecological connectivity modeling, using a least-cost approach that integrates distance, costs, and risks related to barriers. We found that accessibility was contrasted between species, emphasizing the crucial role of the migration type, period, and level of tolerance to low dissolved oxygen values. The highest disruption of ecological connectivity was visible in the 1970s, when the effects of large hypoxic areas were compounded by those of impassable navigation weirs (i.e., without fish passes). As the approach was able to reveal the relative contribution of physical and chemical barriers on overall functional connectivity, it may constitute a model work in assessing the functioning of large river ecosystems.