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Semi-natural woodlands largely characterise Stockport's biodiversity as the borough has the highest proportion of this habitat within Greater Manchester. These tend to have a different character than the north-western acid woodlands found in Bolton and Bury. Many of Stockport's woodlands have been notified as SBIs with a large proportion of these being species-rich, ancient semi-natural woodland including Bramhall & Carr Woods, Poise Brook & Goyt Valley, Norbury Brook & Middlewood, Marple & Torkington Woods, Kirk & River Woods, Marple Dale Wood, Brabyns Wood, Redbrow Wood, Benfield Clough, Windybottom Wood Linnet Clough.

Just over half of Stockport has been identified as open space comprising amenity grassland and agricultural land. A network of freshwater habitats runs through the borough including rivers - the Goyt and Etherow, ponds, lakes, reservoirs and canals. The Peak Forest Canal runs through a largely wooded landscape in contrast to the open moorland and agricultural land the Huddersfield and Rochdale Canals pass through in other parts of the county. To the east of the borough the upland landscape links to the High Peak district providing important breeding grounds for upland birds and a mosaic of upland habitats.