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The South Pennine Moors reach into the north and east of the borough. Like Oldham, the moorland surrounding Rochdale dominates the town and covers a significantly larger area than the urbanised parts of Rochdale. Overall the moorland supports a mosaic of habitats including over 80% of the county's recorded blanket bog in addition to the vast majority of wet modified bog, acidic flush habitats and a significant amount of heathland and upland acid grassland. These habitats together with marshy grassland support important assemblages of upland bird populations for which the South Pennine Moors has been notified as a Special Protection Area.

The Rochdale Canal is also an internationally important site due to the density of the population of floating water plantain which is the highest in the UK. The River Roch, Stanney Brook and Cheesden Brook also run through the borough. Rochdale contains little woodland but that that does occur includes ancient woodland in relatively large blocks such as at the Ashworth Valley.