The study of contamination of sediments of water bodies with chemical elements continues to be one of the important problems of geoecology. The lack of a formal normative base for these indicators has led to different and diverse approaches and methods to solve this problem. The selection of the territory of a large water body on the example of the Volga river basin is made. There are four different hierarchical levels of research objects. The questions of location in time and space of observation points for the change of pollution of the river sediments and reservoirs are considered and justified. Theoretical and methodical substantiation of sampling of these deposits, the allocation of silt fraction less than 0.020 mm, which allows to bring samples containing different size components to the «common denominator» in laboratory studies. The choice of geoaccumulation index as an indicator of the level of pollution of the studied objects is justified. It is recommended at the present stage to use the total index of toxic pollution to assess the total technogenic pressure on the studied area. The assessment of complex pollution of the sediments can also be carried out on the basis of the total toxic pollution. The necessity to use the same permanent set of seven heavy metals Cd, Hg, Pb, Zn, Cu, Cr, Ni and As in solving the problem is substantiated. To present the results of field and laboratory studies, along with traditional tables, diagrams and graphs, it is recommended to use a color scheme map, where the technogenic pressure is displayed from the blue to the green and yellow to the red – the most dangerous. To assess the quality of the sediments for areas of water bodies experiencing anthropogenic load from the 1st – 2nd city-forming enterprises, can be carried out on the mono-element schematic maps or diagrams.