After the end of the Last Glacial Maximum (LGM), Termination I recorded one of the fastest and highest amplitude eustatic oscillations of the Late Quaternary: in less then 15 kyr (between ca. 20 and 5.5 kyr cal. BP) sea level rose ~ 120 m, with at least two steps of increased rate of ice melting and eustatic rise, named Meltwater pulses 1A and 1B. The transgressive sedimentary succession deposited during this interval on several mid-latitude continental margins, among which the central Adriatic margin, includes three distinct units each deposited during a specific interval of the last sea level rise. In particular, the central Adriatic middle TST unit (mTST), composed of two prograding sedimentary wedges separated by an erosional surface, appears the most complex of the three TST units. The mTST unit formed during an interval of extreme climatic instability, including the Bölling-Allerød and the Younger Dryas–Holocene transition. Sequence stratigraphy analyses, integrated by core samples and 14C age estimates, indicate an enhanced sediment flux during the deposition of the mTST unit as a consequence of high-frequency climatic oscillations. Model simulations with Hydrotrend v3.0, a hydrological water balance and transport model, show high rates of sediment delivery within the interval between 13.8 and 11.5 kyr cal. BP as a consequence of increased rates of rainfall and partial melting of the Alpine glaciers. Reconstructions of the sediment architecture using 2D Sedflux 1.0C, a basin-fill model, reproduce the complexity of the internal architecture of the middle TST unit driven primarily by sea level. The internal unconformity within the mTST unit can best be explained by introducing a minor sea level fall during the Younger Dryas. This conclusion is supported by the presence of an extensive barrier–island–lagoon system at −75 m below present sea level, corresponding to the Younger Dryas time interval and representing the best evidence of paleo-shoreline for this interval.