Designated habitats on the 835-hectare Mòine Mhór site include Atlantic salt meadow, intertidal mudflats and sands, degraded (still capable of natural regeneration) and active raised bog. The site is also designated for the species Lutra lutra (Otter) and Euphydryas aurinia (Marsh fritillary butterfly).

Loch Crinan (part of the Mòine Mhór SAC) contains one of the largest expanses of intertidal mudflats and sandflats in western Scotland, encompassing a range of representative brackish sediment habitats and associated communities. The habitat type is particularly unusual for sea lochs on the west coast of Scotland, contributing to the international conservation importance of the site. Much of the intertidal area is mudflat, with sand and gravel in the west and fine silt in the east. On the eastern shore near the mouth of the estuary there are extensive lugworm beds. In the upper parts of the estuary there is a large area of saltmarsh that contains areas of low-mid and mid-upper saltmarsh vegetation, and freshwater transitions. The saltmarsh contains an interesting assemblage of plants, and Loch Crinan is one of the few sites in Britain where the transition from sandflats, to saltmarsh to raised bog can be seen.

Mòine Mhór SAC contains the three attributes associated with otter habitat in Scotland; peatland, freshwater and marine habitat. Holts have been identified in numerous locations in the SAC and although breeding is as yet unconfirmed, it is expected. Large agricultural drains dissecting the raised bog are dammed, providing a freshwater corridor linking all the designated habitats. This network allows otters to move and forage throughout the site undisturbed.

This site is not being actively managed at present but management may be considered in the future.