SUMMARY.Sediment from a precursor of the 2300‐year old Lake Mývatn was traced by diatoms in pseudocrater scoria. This lake (Mývatn I) was deeper than the present Mývatn but similar in size. Tephrochronology confirms an equal age of the Ytrlflói and Sydrifloi basins of the present Mývatn. Diatom succession in the sediment of the Sydriflói basin was divided into four zones, of which the lowest corresponds to inherited and highly disturbed Mývatn I sediment. At 90 cm depth, i.e. around 1600 AD, in the Sydriflói sediment a simultaneous increase occurred inCladophora aegagropila(Chlorophyta),Eurycercus lamellatus(Cladocera) and three diatom species epiphytic onCladophora.The density of Cladocera also followed this trend. The increase in Cladophora was perhaps caused by improved light conditions on the bottom, either because of a decrease in water depth due to sedimentation, or a decrease inAnabaenablooms