The siliceous microfossils—diatom and chrysophycean stomatocystae—of the diatomite and alginite from two maars (Jelsovec and Pincina) of the Late Miocene Podrecany Basalt Formation in Southern Slovakia have been studied. The ecological analysis of the microfossils studied points to a shallow lake environment with ph = 7–8, salinity of 0.3–0.5 %, temperate climate. The nutrient spectrum from the Jelsovec maar where diatomite was deposited suggest an oscillation of oligotrophic and eutrophic conditions. In Pincina maar where alginite was deposited the eutrophic conditions prevailed. The exellent state of Botryococus braunii soft bodies preservation points to a stratified water column in the lake with anaerobic conditions at the bottom. In the Jelsovec maar organic matter is practically missing. The water column was not stratified, even the bottom water was oxygenated and oligotrophic conditions prevailed.