Multiple paleovalley systems of late Quaternary age have been widely explored in previous research from the Gulf of Manfredonia on the basis of seismic data, but only limited information is available on their proximal (onshore) segments. Through an integration of sedimentary, paleoecological (mollusks, benthic foraminifers, ostracods), and geochemical analyses from three 30-50 m-long onshore cores and a sequence-stratigraphic framework chronologically constrained by 25 radiocarbon data, we document the stratigraphic architecture of three contiguous paleovalley systems (Candelaro, Cervaro and Carapelle rivers) and their sedimentary response to Late Pleistocene valley excavation, Holocene filling and basinwide interfluve flooding. Above a prominent sequence boundary formed during the Late Pleistocene relative sea-level fall, fluvial-channel gravels and sands (lowstand systems tract) are overlain by a deepening-upward, valley-fill succession of inner-estuarine (freshwater) to outer-estuarine (brackish) muds (lower transgressive systems tract – TST). The individual valley fills are overlain by laterally extensive bay deposits (upper TST) and by a progradational succession of prodelta/delta front and offshore/shoreface deposits that reflect normal regression under highstand conditions (HST). The transition from fluvial to inner-estuary (fluvial-dominated) and outer-estuary (wave-influenced) deposits records the progressive shift in sediment provenance from Southern Apennine source rocks to a mixed composition that reflects increasing alongshore sediment contribution from northern sources via the SE-directed Western Adriatic Current. The stratigraphic surface that demarcates the transition from estuarine to bay depositional systems (lower/upper TST boundary) represents the physical prolongation of interfluvial terrace surfaces, as valley margins were flooded during the Early Holocene transgression. This surface, typically recognizable on seismic profiles at the boundary between low-amplitude and overlying high-amplitude reflectors, has no obvious lithologic signature in core. However, it can be readily identified on the basis of paleoecologic features (sharp increase in species diversity and in the proportion of marine taxa) that reveal the abrupt transition from laterally confined to unconfined settings.