Palaeoecological analysis of a 3 m sediment core from a coastal site in the western Algarve, near Lagos, Portugal, reveals the changing ecological characteristics of the wetland environment during the late Holocene. The dinoflagellate record and sedimentary characteristics show that approximately 2000 years ago the modern Boca do Rio wetlands were an estuary. By about 1200 14 C years BP, transition to a lower energy environment was taking place. The pollen record at this time indicates the existence of typical salt marsh vegetation. There is a likely hiatus in the sedimentary record caused by the tsunami associated with the Lisbon earthquake of AD 1755. A barrier lake, impounded by tsunami deposits, existed for approximately 60 years before being breached, followed by a reoccurrence of saline conditions. A comparison of the mineral magnetic signature of the sediments with that of soil samples from the catchment suggests a relatively local provenance for some of the sediments, rather than the highly erodible Carboniferous rocks of the Algarve's / / / Serra uplands. However, it is also suggested that there is a biogenic component to the magnetic mineralogy. Coastal wetlands are among the most vulnerable Mediterranean environments. The history and future of the Boca do Rio wetlands is examined in the context of alluviation history, rising sea levels, both past and future, and catchment land use. Changing patterns of cultivation, irrigation and land abandonment during the last 50 years are likely to have increased water demands within the catchment and therefore decreased river discharge to the wetlands. Consequently, the continued existence of the wetlands in their present form is in doubt, despite being part of a protected natural park.