Optimal conditions of sample preparation based on Analytik-Jena and Berghoff applications have been chosen for microwave decomposition of solid environmental samples such as bottom sediments, suspended and solid particles of snow cover in microwave MARS-5. The validity of mercury determination was confirmed by GSO SDPS-1 (State Reference Standard Samples of sod-podzolic sabulous soil) analysis. It has been shown that under studied parameters of microwave decomposition and instrumental determination atomic fluorescence spectrometry is a more preferable method for the determination of mercury in comparison with the atomic absorption method. The analysis of sediment samples has shown that the current level of mercury in Berdsky Bay does not exceed background values for freshwater sediments for all studied hydrological periods. The highest mercury concentration (0,045 μkg/g) was observed in October at the sampling point at the exit of Berdsky Bay. Significant matrix influence causes the necessity to use the stage of concentration on gold sorbent, regardless of mercury concentration in the samples. Additional concentration step is not required for the samples of suspended and particulate matter of snow cover with less organic component content.