The cool, wet climate reduces biological activity and increases leaching of nutrients, which in turn favours the development of acid, peaty soils and peat. The steepness of the slopes has limited the actual amount of peat deposited. True peat is found under cotton-grass bog such as on top of Mullach Mor. It is evident that good burning peats might have been obtained from here, but the islanders preferred to remove the moorland turf nearer at hand; the dried slabs a few inches deep served as fuel, but to the detriment of their pastures. Where this has been done, the soil has washed away, leaving a stony area inhabited, between the rocks, by stragglers from the moorland flora.

Soil formation is also, of course, influenced by the rock chemistry of the island – from the acid granite of Conachair and Oiseval to the basic rocks of the central part of Hirta and the ultra-basic rock of the Mullach Bi ridge. Basic and ultra-basic rocks have much higher calcium and magnesium content that the granite but the availability of such nutrients would be reduced as thicker soil cover developed. Exceptions to this are found in very small patches on unstable slopes of basic rock scree, where downslope movement continually renews the surface horizon to offset leaching by rainwater.

To some extent such effects are countered by the manuring of seabirds and sheep. On Hirta the bird colonies tend to be confined to the cliffs and such enrichment is less pervasive than on the smaller islands of the archipelago. Guano and sheep dung adds nitrogen, phosphate and calcium to the soils while considerable quantities of magnesium, sodium and potassium are continually being added from sea spray. Salt content in the soils is unusually high, from 30 to 320mg/100g compared with only 2mg/100g from an Edinburgh garden. Cultivation by humans (which decreased after 1900 and ceased altogether in 1930) with the addition of organic fertiliser (in the form of human and animal waste, offal and bird carcasses and old thatch) has reduced acidity and improved the structure of the soils around Village Bay, enhancing nutrient content and encouraging earthworms. Nine species have been recorded from Hirta, two of them also occurring on Boreray.

Professor Andy Meharg and a team from Aberdeen University have an on-going programme studying samples of soil from different parts of Hirta, the main island of the St Kilda archipelago. Samples were collected from grazing lands, from fields, and from midden pits where, in the past, waste was collected for manuring. Analysis showed that levels of toxic chemicals from some of the fields and from the pits even now remain at high levels – which may have affected the fertility of the land. The pollutants – including lead, zinc, cadmium and arsenic – can be attributed mainly to the use of seabird carcasses in the manure that was spread across the village fields. Tens of thousands of birds were captured each year, so a considerable amount of waste was generated. Seabirds tend to have elevated levels of a range of potentially toxic metals in their organs. When traveller Martin Martin visited in 1697 he commented on the island's fertility. Adeterioration in the crops is recorded by the mid-18th century. The suggestion is made in this study that this pollution may have caused the reduction in crop quality although there was a general deterioration in climate (often referred to as The Little Ice Age) throughout Britain at this time, with many poor harvests recorded in the Hebrides during the 18th century. This recent work has also provided more information on soil management. Soil was deliberately moved from impoverished areas to the main cultivation places, where instead of a few centimetres the soil has been built up over 1m in parts of the village fields. Landscape-scale movement of soil was not uncommon in the Scottish Highlands and Islands.