We performed a morpho-stratigraphic study of the Tirso River incised valley (Sardinia Island, western Mediterranean Sea), an erosional feature crossing the Sinis fault, a major normal fault bordering the Campidano basin between the Gulf of Oristano and the western Sardinia shelf. High-resolution seismic reflection profiles and multibeam echosounder data, integrated by age-constrained stratigraphic logs derived from 9 sediment cores enabled us to reconstruct the valley evolution during the Holocene. We found that the Tirso valley is the result of a single event of incision and infill during the last eustatic cycle, strongly controlled by the presence of the Sinis fault. In fact, this structure represents a geological threshold that marks an abrupt change in substrate lithology and seabed slope, which controlled the valley morphology, narrow when downcutting early Pliocene formations along the steeper open shelf, and wider inside the Gulf, in the Pleistocene alluvial deposits of the flatter Gulf of Oristano. The sedimentary record starts with alluvial sediments filling the valley along the shelf during the initial phase of sea level rise, i.e., over 10 ka. During the last ~9.0 ka, a bay head delta developed, with the formation of barriers at the gulf entrance. In the mid-late Holocene, the progressive sea-level rise led to rapid drowning of the barrier system, recorded by marine and estuarine sediments filling the valley. Analysis of ecological associations in the cores, collected along a valley-normal transect, allowed for a detailed reconstruction of the paleo-environmental conditions during the latest phase of the incised valley filling controlled by global climatic variations in the Mediterranean region between ~9.0 and ~ 4.5 ka. Together with eustasy, our work reveals that the evolution and sedimentary infill of the Tirso incised valley was strongly controlled by inherited geological constraints, which influenced the morphology of the valley and the stratigraphic pattern.