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Agriculture and the effects of its post-industrial heritage dominate the Wigan landscape. Much of the agricultural landscape has resulted from man's exploitation of the vast peat bogs that would once have covered the area. Pockets of this important habitat remain today with the Borough containing Astley and Bedford Moss which is part of the candidate Special Area of Conservation of "The Manchester Mosses" and is being managed to restore it to active bog. Highfield Moss is also a nationally important site for mixed valley mire communities on peat, unimproved acidic and marshy grassland.

Where the land was once mined for coal, subsidence has resulted in a landscape dominated by network of wetland habitats and reedbeds. These habitats support a wide range of breeding colonies of waterfowl including tufted duck, crested grebe, gadwall, shoveler and pochard and support significant populations of other species such as dragonfly and damselfly. The importance of these sites to biodiversity has been officially recognised by the notification of Bryn Marsh & Ince Moss and Abram Flashes SSSIs. Wigan also contains the "Wigan Pondway", the highest concentration of ponds in the northwest known.

Post-industrial sites have also been colonised by unimproved neutral grassland. The amount of this habitat in Wigan makes up a large proportion of this habitat recorded in Greater Manchester. Wigan also contains a high proportion of Greater Manchester's semi-natural broadleaved woodland much of which has been identified as being ancient including Arley Woods, Atherton & Bedford Woods, Callico & Hullet Hole Woods, Barton Clough, Porter's Wood, Follient Wood, Barrowcroft Wood and Fairclough Wood.