A 341 cm long sediment sequence was recovered from the unofficially named Raffles Sø on Raffles Ø, outer Scoresby Sund region, East Greenland. The sediment sequence consists in the upper part (0–230 cm) of a stratified gyttja enriched in organic carbon and biogenic silica whereas the lower core part (235–341 cm) is composed of terrigenous, consolidated glacio-limnic sediments. 14C-AMS measurements indicate that the sediment sequence represents the entire Holocene lake history from 10,030 calibrated radiocarbon years. The geochemical parameters (opal, total organic carbon (TOC), total nitrogen (TN)) and the total diatom concentration show similar developments during the Holocene, and reflect changes in biological production and nutrient input into the lake. These records clearly reveal a broad Holocene TOC-opal-maximum interval between 5200 and 1800 cal. yrs BP. The diatom flora consisted of 66 taxa representing 20 genera but only seven taxa were abundant and, sometimes, these were monospecifically dominant during the Holocene. In the sediment core from Raffles Sø four successive stratigraphical zones can be distinguished. Accumulation of diatom valves began at 9900 cal. yrs BP with a Stephanodiscus minutulus (Kütz.) Cleve and Möller dominated assemblage (stratigraphic zone 1) followed by a diatom flora dominated by Cyclotella pseudostelligera Hustedt and, less frequently, by Diatoma tenuis Agardh (9400 until 5900 cal. yrs BP, zone 2). Cyclotella sp. A, a taxon which belongs to the Cyclotella rossii-comensis-tripartita-complex, was the dominant floral element between 5200 and 1800 cal. yrs BP (zone 3). From 1800 cal. yrs BP, the periphytic taxa Fragilaria capucina var. gracilis (Østr.) Hustedt and F. capucina var. rumpens (Kütz.) Lange-Bertalot attained highest relative abundances, also almost monospecifically (zone 4). The distribution and composition of the diatom assemblages in the sediment record from Raffles Sø probably reflect past variations in the extent of the lake-ice cover during the growing season. More or less ice-free conditions during summer may have prevailed during the early Holocene until ca. 1800 cal. yrs BP, which allowed growth of planktonic diatoms (Cyclotella taxa) in the pelagic lake region. From 1800 cal. yrs BP, colder conditions lead to a perennial lake-ice cover with a small ice-free moat in summer which favored the growth of periphytic, littoral species (Fragilaria capucina varieties).