With a depth of at least 220 m, Lake Kyaninga is the deepest known maar crater lake in western Uganda. We studied its limnology and phytoplankton community to determine how the frequency and depth of water-column mixing influences nutrient cycling and seasonality in this aquatic ecosystem. Methods Water-column temperature was measured continuously during a full annual cycle between August 2007 and August 2008. Other physical and chemical variables as well as diatom and other phytoplankton communities were investigated on three occasions, namely during the dry season in August of 2007 and 2008, and during the main wet season in April 2009. Key results and conclusions The water column of Lake Kyaninga is permanently stratified (meromictic) below ~ 100 m depth. Above this depth, mixing frequency varies from daily (down to 8 12 m depth) over at least once per year (down to 39 47 m depth), to once in several years or decades (between 39 47 and ~100 m depth). Nutrient and chlorophyll concentrations as well as phytoplankton data classify the lake as low in aquatic productivity (oligotrophic). Its pelagic, open-water phytoplankton community is dominated by Cyanobacteria (blue-green algae) and Chlorophyta (green algae). Bacillariophyta (diatoms) contribute only a minor part of total phytoplankton biomass in both wet and dry seasons, and are characterized by an assemblage of small Nitzschia species. Epiphytic and epipelic diatoms are relatively few, because steep rocky crater slopes limit the littoral zone even though water-column transparency is high. The composition of recently deposited diatom assemblages preserved in offshore surface sediments gives a good, annually integrated representation of the present-day pelagic diatom community. The documented species richness of the diatom flora of Lake Kyaninga is moderate with about 150 taxa. Only ~ 17% of these are biogeographically restricted to tropical Africa; and most of these belong to the genus Nitzschia.