In coastal areas, under a context of relative sea-level stability during the past 6,000 years, one important question relates to the impact of environmental conditions on human settlements around lagoons. Historiography has developed a number of deterministic models but how do these fair in the light of recent palaeo-environmental data? What was the impact of these occupations on the evolution of the coastline? How did ancient societies use and overcome, or not, the environmental potentialities and specific constraints linked to the occupation of lagoonal environments, including accessibility, navigation conditions, sediment infilling and the draught depth. Here we present a number of multidisciplinary case study examples of lagoonal harbours. We attempt to estimate the weight of natural forcing agents on the different harbour sites and underline the important roles of coastline changes and the sedimentary infilling of the lagoons at different spatial scales. These processes impacted upon the infrastructure and the viability of the lagoonal harbours to varying degrees. We present five main types of lagoonal harbour that show the great diversity of these environments, their potentiality and also their constraints: (1) artificially-dug lagoonal harbours, known in the ancient literature as "cothons", (2) infilled lagoonal harbours in deltaic contexts, (3) lagoonal harbours still in water, (4) estuarine harbours and (5) mixed lagoon systems.