The loch was designated a National Nature Reserve (NNR) in 1998, and is managed by a partnership between NatureScot, the Scottish Wildlife Trust (SWT) and Sutherland Estates.

[4] Beneath the sand dunes lies a bedrock of old Red Sandstone, overlain by shingle ridges, which extend from the western NNR boundary to the current coastline and north from Littleferry to Golspie.

The pinewoods hold species including crossbills, siskin, common redstart, treecreeper, great spotted woodpecker, buzzard and sparrowhawk.

Otter and pipistrelle bats are also found here, along with other typical Scottish land mammals such as roe deer, fox, pine marten, and weasel.

The most noteworthy flora is that of the pinewood at Balblair Wood, where the nationally important species one-flowered wintergreen, twinflower and creeping lady's-tresses can be found.

[7] Loch Fleet became a nature reserve under the management of the Scottish Wildlife Trust in 1970 by agreement with the landowners, Sutherland and Cambusmore Estates.

The SPA covers 7,836.33 hectares (19,364 acres) of Loch Fleet, the Dornoch Firth, Morrich More, the Mound Alderwoods and Tarbat Ness, and was also listed as a Ramsar site the same year.