The northern Bay of Biscay has previously proven its great potential for recording the ‘Fleuve Manche’ paleoriver (i.e., the largest Pleistocene river in Europe) fluvio-glacial activity. In this study, new dinoflagellate cyst (dinocyst) analyses have been carried out at sub-centennial resolution in core MD13–3438 to reconstruct the deglacial history of the ‘Fleuve Manche’ paleoriver runoff coupled with European Ice Sheets (EIS) fluctuations across Heinrich Stadial 1 (HS1: 18.2–14.6 ka BP), a key extreme climatic event of the last glacial period. Prior to Heinrich Event (HE) 1 (16.7–14.6 ka BP), the onset of HS1 (18.2–16.7 ka BP) appears here marked by enhanced ‘Fleuve Manche’ paleoriver runoff, materialized by laminated deposits. Our work suggests a novel sub-centennial scale subdivision of the early HS1 (laminated) interval into 5 sub-phases when episodes of substantial fluvio-glacial delivery concomitant with warm summers alternate with episodes of moderate runoff associated with extended cold winters. We argue that multidecadal seasonal changes played a key role in the hydrological regime of western Europe during this HS1 interval, with the retreat of the southern limb of the EIS, and associated influx of meltwater and fluvio-glacial delivery, which were strongly influenced by those multidecadal changes in seasonality. Interestingly, our paleoclimatic record not only evidences the crucial role of seasonality in controlling climate and hydrological variations during HS1 but also shows a remarkable echo with reconstructions from the western Mediterranean Basin, highlighting common climate forcings at regional scale during the last deglaciation.