Detailed work on the blanket peat of northern Scotland has revealed an environmental history of some of the most extensive bogs in western Europe, covering 4000 km². Charman (1995) suggests that, although there is much variations between sites, a common sequence of development can be identified:

1. early formation of peat commenced in moist hollows, perhaps with shallow pools
2. the establishment of a sedge fen, with reeds, and birch growing nearby. The bogs remain isolated one from another.
3. an ombrotrophic phase, when the bog is fed only by nutrients in rainwater. The bog surface dries out, heathers become established and the peat is increasingly humified. Blanket peat is finally established across the terrain.
4. the re-establishment of fen peat, to give The Flows as we see them today.

The total thickness of peat may exceed 5 m and represent over 11, 000 years of organic accumulation. The sequence of changes may be understood against a background of climate change, vegetation succession, soil development and human impacts.

Stage 1 dates from the Lateglacial and early Holocene, the period between the retreat of the last ice sheet and 9000-7000 years ago - the timings of changes vary between bogs. The mires were dominated by mosses, notably Sphagnum. Stage 2 commences after 9000 yr BP and extends to 6400 - it can be recognised in deep peat cuttings by the remains of birch bark, twigs and stumps. Stage 3 commences around 6400 yr BP and continues until 2850 yr BP - this drying phase in the peatlands coincides with the appearance of charcoal fragments in the peat cores, indicating periodic burning of the bog surface. Stage 4, establishing The Flows and their lochans, is surprisingly late and spans only the last 3 thousand years.

The bog systems do not appear to be responding simply to the climate changes of the Holocene. The drying of the peatland is out of phase with the postglacial climatic optimum from ~7000-5000 yr BP and the return of the fen peat occurs after the climate has cooled and precipitation increased. The changes appear instead to relate to the hydrology of the bogs and to be partly self-regulating. The development of blanket bog has taken over 4000 years in Caithness but then created a largely unbroken peat surface. Until around 3000 years ago the bog was able to maintain a level of internal drainage sufficient to allow the surface to remain relatively dry. Thereafter the water table rose, perhaps as peat reached a critical thickness over the terrain, and fen peat returned.