Lake Tovel is an oligotrophic, meromictic, mountain lake of the Dolomites that undergoes marked seasonal water-level fluctuations (WLFs). We used neo- and paleolimnological data collected since 1999 to test the utility of algal and cyanobacterial pigments and diatom and chironomid biodiversity as proxies for WLF and to highlight the contribution of benthic algae to the sediment record. We found that detailed knowledge of presentday spatiotemporal patterns of WLF is essential for a complete and correct interpretation of paleolimnological data. Scytonemin, a cyanobacteria-specific photoprotective pigment, was produced by epilithic cyanobacteria in the depth zone affected by WLF and should be considered a proxy for the extent of WLF. The phytobenthos was as important as phytoplankton as a source of sedimentary pigments. We used information gained on the detailed distribution of diatoms at different depths and on different substrata in the 2 basins to show the probable location in the lake from which taxa in sediment cores originated to aid in interpretation of the sediment archive (including identification of periods of active hydrology). We sampled present-day chironomids in springs and streams feeding the lake and along a depth transect in the main basin. The taxa found were all rheophilic, crenophilous, or typical of the littoral zone of oligotrophic lakes. We interpreted sections of the cores containing large numbers of Orthocladiinae and Diamesinae head capsules as indicative of periods of active hydrology (including sudden and marked WLF) because the littoral taxa found in the cores must have been derived from the littoral zone by sediment focusing or slumps. Thus, we identified useful proxies of WLF in mountain, carbonate lakes.