The following is a list of Sites of Special Scientific Interest in the Annandale and Eskdale Area of Search. For other areas, see List of SSSIs by Area of Search.
- Bell's Flow
- Bigholms Burn
- Castle Loch
- Dryfe Water
- Langholm - Newcastleton Hills
- Loch Wood
- Lochmaben Lochs
- Moffat Hills
- Penton Linns
- Perchhall Loch
- Raeburn Flow
- River Esk, Glencartholm
- River Tweed
- Royal Ordnance Powfoot
- Upper Solway Flats and Marshes