Seismic surveys with sub‐bottom profiler were carried out in the Manfredonia Gulf in the southern Adriatic Sea. Here, a buried surface was recognized on which three valleys, located about 80 km from the shelf edge, were deeply incised. Beneath this surface, a pre‐upper Würm seismic unit (PW) was identified. Above, two seismic units were recognized: the transgressive system tract (TST) and highstand system tract (g2). On the basis of regional correlation with onshore and offshore data, these units and their boundaries were dated and correlated with phases of the last glacial–interglacial cycle. The incised valley system was attributed to the Marine Isotopic Stage (MIS) 2. The TST and g2 units fill the valleys and were attributed to the post‐glacial sea‐level rise and highstand. The incised valleys are anomalous with respect to published models; despite having many characteristics that would have limited the fluvial incision (the lowstand shoreline that remained on the shelf, the low gradient of the shelf, the subsidence that affected the study area since MIS 5), the valleys appear to be deeply incised on the shelf, with valley flanks that can exceed 40 m in height. The model to explain the formation of the valleys comprises enhanced river discharge as the key factor in increasing river energy and promoting erosion across the low gradient shelf. Copyright © 2014 John Wiley & Sons, Ltd.