Abstract Deep‐water of the eastern Mediterranean basins mainly forms in the Adriatic Sea and episodically in the Aegean Sea. However, past and future variability under changing temperature and freshwater inputs remains unclear. We reconstruct seawater εNd from Northern Ionian Sea cores to trace intermediate‐ and deep‐water provenance during the Holocene. High organic matter deposition during S1a and S1b corresponds to radiogenic εNd values (up to −4.9), indicating reduced and shallower Adriatic Deep Water (AdDW) formation, with Ionian Sea increasingly dominated by Aegean deep water (AeDW). The re‐ventilation of deep‐water at ∼8.2 ka is marked by unradiogenic εNd (−6.5), implying active AdDW formation. In contrast, a second re‐ventilation within the S1b at intermediate depth is associated with radiogenic εNd values (−4.5) attributed to the formation of the radiogenic intermediate water from the eastern basin (LIW). These results demonstrate the high sensitivity of Mediterranean deep‐water formation to freshwater forcing and abrupt climate change.