Abstract Combined mineral magnetic, geochemical and palynological analyses were undertaken on Holocene sediment sequences recovered from lakes in the Abisko region of northern Sweden. The absence of the Kårsa glacier in the Early and Mid‐Holocene is reflected in downstream lake sediment sequences by zones of gyttja clay that experienced post‐depositional magnetite (Fe3O4) dissolution and greigite (Fe3S4) authi‐genesis, due to organic matter decomposition and sulphate reduction. Between 3,000 and 2,500 14C yrs BP the Kårsa glacier reformed and the accumulation of sediment with a higher minerogenic content took place, with the result that magnetite was preserved in the sediments. The mineral magnetic properties of different sediment types (algal/detrital gyttja) deposited in two lakes in the Abisko valley record the same climatic deterioration between 3,000 and 2,500 14C yrs BP, although these lakes have been isolated from a glacial influence during the Holocene. Gyttja deposited during the Early and Mid‐Holocene was also subjected to magnetite dissolution (and greigite authigenesis in one lake) until the regional climate deteriorated between 3,000 and 2,50014C years BP. Due to climate induced alterations in vegetation the limnology of the lakes changed and magnetite became preserved in the sediments. Snowball, I.F., 1996: Holocene environmental change in the Abisko region of northern Sweden recorded by the mineral magnetic stratigraphy of lake sediments. GFF, Vol. 118 (Pt. 1, March), pp. 9–17. Stockholm. ISSN 1103–5897.