Mollusks recovered from three cores taken from the Cananéia-Iguape estuarine-lagoonal system (São Paulo State, Brazil) were studied. The sampled sediments cover a period beginning approximately two centuries ago and end at the present, including a period when the system suffered significant changes of anthropogenic origin – that is, the construction of an artificial channel connecting the lagoon with a nearby river and with the resulting input of fresh water and contaminants generated from mining activity upstream. The mollusk composition reflects these changes. The more abrupt changes in this composition coincide with the opening of the Valo Grande artificial channel in 1852. Another significant but minor change event was verified for around 1977± one year in areas that were not previously affected, perhaps showing the effect of the closing and reopening of the channel.