Heavy metals which pollute aquatic environments typically bond with bottom sediments and the analysis of the spatial distribution of metals allows to assess the geochemical purity of deposits and to identify the potential pollution sources. Research carried out on the Wigry Lake involved the collection of almost 500 samples of sediments, and the specification of the depth of their residence (0.2-71.4 m) as well as the level of concentration of three metals: Fe (80.3-32 857 mg kg), Mn (17.8-1698 mg kg) and Zn (3.14-632 mg kg). The geochemical and bathymetric data was interpolated using geostatistical methods and mapped with the consideration of 5 types of sediments: lacustrine chalk, carbonate gyttja, fluvial-lacustrine sediment, organic gyttja and clastic sediment. As a result, a significant increase in the concentration of metals was revealed in deeper zones, at a considerable distance from the lake shore, wherein the respective values of correlation coefficients were as follows: depth-Mn 0.77; depth-Fe 0.60; depth-Zn 0.58. A strong dependency between the concentration of analysed metals and the type of sediment, attributed to the granular and chemical composition of sediments, was also revealed. Correlations between individual metallic pairs (Fe-Mn 0.77; Fe-Zn 0.80; Mn-Zn 0.75) indicated that similar factors influence spatial distribution of metals in sediments. The implementation of 3 different geochemical backgrounds allowed to conclude that the Wigry Lake is slightly polluted with the analysed metals, and that the origin of Mn is mainly natural, while in the case of Fe and Zn anthropogenic influence can also be identified.