The Cork Harbour Bird Atlas contains information on 25 years of bird counting effort within Cork Harbour. The Atlas contains data on trends for specific species. The Atlas also contains information on the most commoly seen species within the Harbour. Click here to view the Bird Atlas.

For natural history enthusiasts, the entire Cork Harbour is of major international importance for waders (20,000) and wildfowl (5,000), particularly winter migrants, which are supported by its extensive mudflat areas around Lough Mahon, the Douglas Estuary and the North Channel, Lough Beg, Saleen, Rostellan and Whitegate. Cork Harbour hosts the largest number of wintering birds in any area on the east and south east coasts of Ireland. It is designated as both a Special Protection Area for birds and a Ramsar site of international importance for this reason (See below).

Other designations within the Harbour protect important habitats of salt marsh, reedbed and intertidal mudflat. They include proposed Natural Heritage Areas (Douglas Estuary, Great Island Channel, Lough Beg, Rostellan Lough/Aghada Shore/Poulnabibe inlet, Whitegate Bay, Cuskinny Marsh), and candidate Special Areas of Conservation (Great Island Channel). The River Lee is also designated as a salmonoid river under the EU Freshwater Fish Directive.

This implies there is an obligation to maintain specific water quality standards and to control pollution in this area. Protected fauna include the otter (Lutra lutra), the grey seal (Halichoerus grypus) and the common seal (Phoca vitulina). Cetaceans such as common dolphins (Delphinus delphina) and bottlenose dolphins (Tursiops truncatus) are occasionally sighted in the Harbour. In Summer 2001, the arrival of a pod of three Orca whales (Orcinus orca) in Cork Harbour attracted great attention from local spectators and national media.