Consecutively to the global sea-level rise, coastal landscapes significantly changed during the Early Holocene. We explored how coastal mutations have affected ancient human systems in the western Mediterranean. The Pego-Oliva basin (Spain) provides a thick sediment sequence located in proximity to two well-studied Mesolithic and Neolithic archaeological sites. Based on 16 sediment cores, sedimentological analyses, 14C dates, and integration of previous works, we reconstructed the architecture of the sedimentary facies and the chronology of deposition for the last 9500 years. From 9500 to 8200 cal. BP, the stepwise inland migration of the coastline is characterised by the deposition of peat layers at distinct depths indicating four phases of barrier-lagoon systems development. The marine transgression caused the disappearance of the lagoon at 8200 cal. BP, and reached a maximum inland position at 7300 cal. BP. Since 5800 cal. BP, sea-level stabilisation induced coastal progradation and barrier-lagoon system construction. Five marine flooding phases dated at 9500, 9100–9000, 8750–8650, 8450–8200, and 8100–7300 cal. BP match Atlantic meltwater pulses. Comparison to archaeology shows that the long-lasting Mesolithic occupation corresponds to the presence of coastal offering easily exploitable local intertidal resources. In contrast, during the Late Mesolithic, we observe a lagoon contraction and the reduction of lagoon bivalves size arguing for a decrease in resource productivity. This changes in the lagoon ecosystems negatively impacted to Late Mesolithic populations leading to a less intense occupation of this area. Therefore, the 700 years' temporal hiatus between the last hunter-gatherers and the first farmers occupying this area is explained by the disappearance of the formerly exploited biotopes because of sea-level rise, a situation that may have been aggravated by coincidence of the 8200 cal. BP climate event. The maximal sea transgression corresponded to a shift from intertidal to infralittoral species between the Impressa/Precardial and the Postcardial Neolithic, indicating a good adaptation to changing environments at that time. However, comparison between Late Mesolithic to Early Neolithic suggests that communities with different cultural baggage have had a different perception of the same environment. By the past perspective, it emphasises that perception of the ecosystem value as a benefit or constraint, and of the risks associated with sea-level rise, relies first on the local and regional scales adaptive capacity of society to global changes.