The estuary is particularly important for its wintering bird populations and both waders and wildfowl achieve numbers each year that are of international importance.

Internationally important populations of wader species such as Oystercatcher, Knot, Curlew, Redshank and Grey Plover, amongst others, are supported. These birds feed on the abundant invertebrate numbers found on the extensive intertidal flats. They also make extensive use of the coastal grazing marshes and fields around the estuary for feeding and roosting.

The estuary also contains a number of high tide roost sites that are great for birdwatching, such as Hilbre Island, the foreshore at West Kirby, the shingle spit at Point of Ayr and the salt marshes at Oakenholt.

As a staging post for migrating birds in both spring and autumn, the Dee is also an important place. Nationally important numbers of Ringed Plover are regularly seen on passage and, in addition, the summering flock of non-breeding Black-tailed Godwit, one of the largest in the UK, is regarded as of national importance.