Northern peatlands are estimated to store up to one third of all terrestrial carbon as peat and, even though a large extent of boreal peatlands is in pristine condition, extensive areas have been affected by natural or anthropogenic disturbance. Here, we aimed to study the bulk organic matter, elemental composition and molecular inventory of a peat disturbed by a clay deposit in the mesotelm layer (from −35 to −45 cm) due to mining activity near the peatland zone. We therefore investigated loss on ignition, elemental analysis, lignin monomers and non-cellulose carbohydrates, as well as the lipid fraction. In general, no significant impact on peatland evolution was noted, the only odd result being an increase in complex lipids containing acyl groups in the clay deposit zone, although this did not influence the distributions of the fatty acids, which had a bimodal distribution at C₁₆ and C₂₄/C₂₆, typical of a non-impacted Sphagnum dominated peatland. Phospholipid analysis showed an increase in the quantity of mid-chain branched fatty acids, suggesting high sulfate reducing activity in the underlying clay deposit. Other lipid, lignin and carbohydrate biomarkers showed a normal peatland evolution, plant deposition being apparent in the bottom layer designated by the catotelm and microbial activity and production being highest in the upper layer, represented by the acrotelm and mesotelm.