The siliceous microfossils – diatom and chrysophycean stomatocystae – of the diatomite and alginite from two maars (Jelšovec and Pinciná) of the Late Miocene Podrečany 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 Jelšovec maar where diatomite was deposited suggest an oscillation of oligotrophic and eutrophic conditions. In Pinciná 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 Jelšovec maar organic matter is practically missing. The water column was not stratified, even the bottom water was oxygenated and oligotrophic conditions prevailed.