A mid- to late-Holocene paleohydrological reconstruction from the northeast Atlantic is proposed through the study of a high-resolution sedimentary record from the northern continental shelf of the Bay of Biscay (BoB). Three foraminiferal species dominate the assemblages with Rosalina globularis showing an overall decrease in absolute and relative abundances from ~7 to 0.4 cal. ka BP, whereas the opposite trend is observed for Cibicides refulgens and Lobatula. These long-term patterns are interpreted as a response to the overall cooling trend and/or the progressive deepening of the water column because of the relative sea-level (RSL) rise. Foraminiferal δ18O and grain-size analyses show a significant shift around 3.5–2.5 cal. ka BP toward a heavier isotopic signature and finer sediments. We mainly link this change to enhanced contribution of continental freshwaters and fine sediments after the near-stabilization of the RSL rise. By reducing coastal accommodation spaces, this led to a better channelization of river outflows and probably to the formation of the modern winter thermohaline front. Superimposed on these long-term patterns, our data highlight strong millennial-scale variability (1250-year peak). Such cyclicity is consistent with several records tracing changes in rainfall and storminess regimes in northern Europe, and the dynamics of the subpolar gyre (SPG). We suggest a millennial time-scale control of a NAO-like (North Atlantic Oscillation) climatic process modulating continental humidity (and the associated river discharges) and SPG dynamics through wind stress. Spectral analyses reveal an additional 500-year frequency peak implying a possible solar forcing.