Ancient lake sediments provide opportunities to reconstruct aquatic ecosystems during previous interglacials. In the summer of 2010, the ICDP project PALEOVAN drilled a complete succession of the lacustrine sedimentary sequence deposited during the last *600,000 years in Lake Van, eastern Anatolia (Turkey). Previous palaeolimnological analysis of the Lake Van sediment record has shown diatoms to be absent over most of the sequence apart from a short interval during the Holocene. Here, we demonstrate the preservation of additional fragmentary diatom records during Marine Isotope Stage , each spanning no more than a few thousand years. Although brief, the presence of contrasting diatom assemblages between these two interglacials provide a snapshot of varying water depth and, by inference, climate. Analysis of MIS7e samples suggests that lake water levels were low after a period when the lake was open (i.e., high lake levels with the presence of an outflow present), resulting in higher salinities and possibly less stable bottom waters, which switched between anoxic and oxic states more frequently. By contrast, the diatom assemblages during MIS5e are characteristic of fresh, relatively nutrient rich waters. This suggests that lake levels were high, that the lake was hydrologically open with an outlet, and that the bottom waters were anoxic for long periods of time. Furthermore, our palaeoconductivity estimates and modelling of the past lake volumes with respect to its salt content support the presence of an outflow.