The source of the Nairn is not in the county which borrows its name but in the Monadhliath Mountains of Inverness-shire. The headwaters of the Nairn, the Allt Mor and Crom-allt Beag drop steeply down the western slopes of Càrn Ghriogair, their combined waters flowing beneath the B851 road and turning northeastwards. They young River Nairn is soon joined by the diminutive River Brin on the right bank and later by a burn draining the sizeable Loch Duntelchaig on the left. The River Farnack is the next right-bank tributary, followed by the Craggie Burn near where the A9 road crosses the Nairn at Daviot, Inverness-shire.
Soon below Culloden Moor, the Nairn passes beneath the Culloden Viaduct carrying the mainline railway between Perth and Inverness. Then it becomes the county boundary between Inverness-shire and Nairnshire for a while before entering Nairnshire entirely.
The river runs between Culloden Forest and Assich Forest to pass beneath the B9090 road between Clephanton and Cawdor. Its last major tributary, the Allt Dearg joins from the right and the river continues northeastwards passing beneath the B9090 once again before reaching the town of Nairn.
At Nairn, the river enters the Moray Firth.
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