Small shallow lakes are a characteristic feature of blanket bog habitats. The biotic assemblages of these lakes can be particularly species rich, especially in terms of the aquatic invertebrate fauna. Despite their potential conservation value, relatively little is known about their physico-chemical or biological characteristics in northern Europe in comparison to other freshwater habitats, and their undisturbed reference conditions are still unknown in Ireland. We surveyed upland and lowland blanket bog lakes, across both sedimentary (sandstone) and igneous (granite) geologies, to compare baseline physico-chemical and biological conditions for blanket bog lakes in western Ireland. A comprehensive data set of water chemistry, Chydoridae, littoral macroinvertebrates and aquatic macrophyte taxa were collected from all lakes over a twelve-month period beginning in March 2009. The main difference in lake hydrochemistry was that the lowland lakes, situated at lower altitude and in closer proximity to the coast than the upland lakes, had significantly higher conductivity and major ion (sodium [Na], chloride [Cl], magnesium [Mg], potassium [K] and sulphate [SO4]) concentrations because of the greater influence of atmospheric (sea spray) deposition. The upland lakes were also significantly cooler and had higher concentrations of total phosphorus (TP). Differences were also evident between the upland and lowland lakes in the chydorid, littoral macroinvertebrate and macrophyte communities, primarily caused by marine-driven hydrochemical variation and differences in benthic substrate. The chemical effect of marine deposition appeared to have a much greater impact on lake hydrochemistry and biology than either underlying geology or altitude. This is the first study of its kind to be carried out on blanket bog lakes in Ireland. More information is needed on the biology of such lakes, together with research on anthropogenic drivers of biotic communities, if significant loss of biodiversity associated with agriculture, peat extraction, burning, wind farm developments and conifer afforestation is to be prevented.