The majority of the intertidal of all the islands, stacs and skerries are extremely exposed to wave action and the influence of the almost constant oceanic swell. Some small areas such as Village Bay are relatively less exposed and this is reflected in a slightly different flora and fauna.

Typically the intertidal comprises vertical or near vertical bedrock; in a few places small horizontal platforms/ledges occur on which there are some shallow rock pools that support a specialised fauna and flora. The classical intertidal zonation pattern of communities reflecting the duration of emersion is greatly extended above Mean High Water Spring Tide (MHWS) mark due to the effects of wave splash and swell. The supralittoral typically extends up to 20m above MHWS mark and exceptionally to 50-100m on some of the most exposed westerly/north-westerly facing cliffs.

The supralittoral comprises a very broad band of lichen dominated rock characterised by extensive growths of the encrusting black lichen (Verrucaria maura) and various foliose yellow, orange and grey lichens. Areas of the rock surface enriched by nitrate derived from guano produced by the many thousands of roosting and nesting seabirds support very dense growths of the tufty green alga Prasiola stipitata. In other areas the ephemeral red alga, Porphyra umbilicalis covers the rock in a band, up to 4m wide, of glistening, ruby-red sheets. Very few animals are able to survive in these conditions, with only the occasional barnacle and small limpet and various tiny winkles that are able to find some shelter in the small cracks and crevices etched in the rock surface.

Boreray IntertidalThe eulittoral zone is characterised by different mixtures of a small number of biotopes that reflect subtle variations in the local topography. Nonetheless they are all typical of the highly wave exposed nature of the area and whilst they are relatively species poor, animal dominated, they do include some constituent species considered rare in the UK and further afield.

The majority of the upper eulittoral zone is colonised by either barnacles (Chthamalus montagui and Semibalanus balanoides) that form a broad grey-white band, or in the more exposed areas, by a dark blue-black band of small blue mussels. Limpets are interspersed amongst the barnacles and the uniformity of the white band is interrupted by patches of black tufted lichen (Lichina pygmaea) and in the comparative shelter of any crack or crevice occasional clumps of small red algae (e.g. Mastocarpus stellatus, Osmundea pygmaea). Amongst the mussels, various small red algae (e.g. Ceramium shuttleworthianum, Corallina officinalis, Mastocarpus stellatus) can be found and in some places the mussels are covered by a thin clingfilm-like wrapping of Porphyra sp. At some of the most exposed locations above the main mussel band there is a narrow band of rare, highly specialised algae – Fucus distichus and Fucus spiralis var nana. These species have very restricted distributions in the UK, being confined to the most exposed areas of the far north and west coasts of Scotland. The specialised, almost bladderless form of bladder wrack (Fucus vesiculosus f. linearis) also occurs in a narrow band in places below the F. distichus band. Towards the bottom of the eulittoral zone, the barnacles and mussels give way to a dense turf of Mastocarpus stellatus under which there is a variety of other algae including Palmaria palmata,
Corallina officinalis and Osmundea pinnatifida and encrusting corallines. Extensive growths of M. stellatus as seen at St Kilda are scarce elsewhere in the UK. In other parts, the lower eulittoral is characterised by growths of the surge tolerant brown alga, thongweed with its characteristic buttons and straps. There is an understorey of red algae and where there is sufficient shelter from the surge various small animals including anemones and gastropods are found.

The sublittoral fringe and the upper infralittoral are dominated by surge tolerant kelp species, principally dabberlocks with its narrow midrib and thin wavy frond, which is ideally adapted to survive the constant wave surge. The rock beneath is covered by a startling pink covering of coralline algae creating a dramatic visual contrast with the orange-brown of the dabberlocks. In some places where there is comparative shelter, although still wave-exposed, the dominance of the dabberlocks is replaced by a mixture of dabberlocks and tangle and as well as the encrusting coralline algae there is a diverse array of foliose red algae (e.g. Palmaria palmata, Corallina officinalis, Mastocarpus stellatus, Lomentaria articulata). The effects of the surge extend to considerable depths and the dabberlocks communities persist to depths of around 15m, much deeper than is typical (i.e. 5m) in other parts of the UK.

The constant action of the sea has resulted in the formation of partially exposed caves and overhangs. The ceilings and walls of these are constantly damp from the effects of the swell and spray and support luxuriant growths of animals such as anemones, sponges and the orange hydroid Tubularia indivisa normally only found in the infralittoral.