The depth-distribution of epilithic diatoms in a carbonate meromictic lake (south-eastern Alps), characterized by marked water-level fluctuations, was investigated. Fixed stations were placed along a depth-profile at intervals of 2-3 m and sampled throughout the year using scuba diving. Diatom analysis included quantification of living cells (biovolume calculations) and the estimation of fucoxanthin concentration, which, coupled with the analysis of digested material, permitted taxonomic determination at specific or subspecific level. Multivariate analyses indicated the following variables to be significant: water-level fluctuations, photosynthetically active radiation, silica and nitrates. Diatoms had distinct depth-distributions. Quantification of densities, biovolumes and Chl a, and physiological (senescence index, fucoxanthin), functional (photosynthetic efficiency), and community structure (diversity) parameters allowed the definition of three depth-distribution zones (shallow, mid-depth and deep). The different diatom communities in these zones were confirmed by ANOSIM (analysis of similarity). The shallow, mid-depth, and deep zone were characterized by disturbance due to water-level fluctuations, high stability with favourable growth conditions and severe light limitation, respectively. Community composition and diversity depth-distribution features remained relatively stable throughout the year, while marked changes in benthic diatom biovolumes were modulated by competition for light with phytoplankton. Fucoxanthin was strongly correlated with epilithic diatom biovolumes. The results indicate that depth-distribution patterns should be considered when performing lake diatom biodiversity inventories and integrity evaluations because water-level fluctuations are likely to increase in many lakes due to increased withdrawal of water and climate change in the future.