Beirut, Sidon and Tyre were major centres of maritime trade from the Bronze Age onwards. This economic prosperity generated increased pressures on the local environment, through urbanization and harbour development. Until now, however, the impact of expanding seaport infrastructure has largely been neglected and there is a paucity of data concerning the environmental stresses caused by these new forms of anthropogenic impacts. Sediment archives from Beirut, Sidon and Tyre are key to understanding human impacts in harbour areas because: (i) they lie at the heart of ancient trade networks; (ii) they encompass the emergence of early maritime infrastructure; and (iii) they enable human alterations of coastal areas to be characterized over long timescales. Here we report multivariate analyses of litho- and biostratigraphic data to probe human stressors in the context of their evolving seaport technologies. The statistical outcomes show a notable break between natural and artificial sedimentation that began during the Iron Age. Three anchorage phases can be distinguished: (i) Bronze Age proto-harbours that correspond to natural anchorages, with minor human impacts; (ii) semi-artificial Iron Age harbours, with stratigraphic evidence for artificial reinforcement of the natural endowments; and (iii) heavy human impacts leading to completely artificial Roman and Byzantine harbours.