The estuary of the lower River Murray features a complex mosaic of lakes, coastal lagoons and interconnecting channels. The waters of these wetlands are degraded as a result of river regulation, water abstraction, salinisation, sedimentation and the recent constriction of the River mouth. Palaeolimnologial analysis of sediment cores in two wetlands reveals that salinity in the large terminal Lake Alexandrina was only moderately influenced by tidal inflow, particularly over the past ca. 2000 years. It is now largely fresh as a result of isolation by a series of barriers completed by 1940 AD. In contrast, the seaward portion of the Coorong, a back barrier coastal lagoon, was determined to be a subsaline estuary strongly influenced by marine inflows. These findings contrast somewhat with the Coorong's current Ramsar classification as a saline lagoon. Riverine diatoms, typical of the fossil flora of Lake Alexandrina, are rare or absent in the Holocene sediments of the Coorong, other than for a short period in the late Holocene in the northernmost end of the lagoon. The palaeolimnological evidence for independent evolution of these wetlands is consistent with geomorphic evidence of a stranded, last interglacial shoreline that acted as a sill limiting the exchange of flows between Lake Alexandrina and the Coorong lagoon.