Oysters have been harvested from the estuary for more than a thousand years and there are remains of fish weirs from the Anglo-Saxon era. At the head of the estuary is the town of Maldon, which is a centre of salt production. The other major settlement is the town West Mersea, of Mersea Island, on the northern seaward side. Numerous other villages are on its banks.
Within the estuary is Northey Island which was the location for the first experiments in the UK in 'managed retreat', i.e. creating saltmarsh by setting sea walls back from what are perceived to be unsustainable positions. The area is notable as a breeding area for little tern (Sternula albifrons) and as a transit point for ringed plover (Charadrius hiaticula).
^"Blackwater Estuary citation"(PDF). Sites of Special Scientific Interest. Natural England. Archived from the original(PDF) on 8 December 2015. Retrieved 28 November 2015.