Variation of the chemical composition of bottom sediments collected from three lakes with different water mixis, morphometric parameters, catchment areas and anthropogenic pressures was analyzed. Sediment samples were characterized by water content and concentrations of organic matter, nitrogen, phosphorus, calcium, iron and aluminium. Statistically significant correlations between the content of organic matter, nitrogen and phosphorus were found. In a large and deep lake (dimictic) subjected to limited human impact, the tendency changes of chemical composition along the sediment profile indicates a recent considerable increase in water trophy. In a small mid-forest lake (classified as meromictic), the changes in chemical composition of bottom sediments along with depth point to periodical increases in fertility as a result of wastewater inflow. In a large mid-field lake (polymictic), the analogous variation has indicated disturbances in the mechanism of sediment formation.