The work aimed to study the geochemical transformation of the lake under sediment transport from the catchment. The study used a catenary complex approach based on the basin principle. The selected urban catchments had different functional landscape areas where contemporary sedimentation processes occur: carriageway, sidewalk, lawn, park/forest edge, beach, playground or sports ground, and parking lot. A sampling of environmental compartments was carried out in different functional landscape zones of catchments and on lakes in warm and cold periods of the year. In total, 28 samples of environmental compartments were collected from two catchments in warm and cold seasons, 18 samples of ice, water, and snow were collected on the lakes in the winter season, and 15 cores of bottom sediments. The cation and anion composition, pH, Eh, elements’ concentrations, mineral composition, Pb isotopes, and concentration of technogenic radioactive isotope Cs-137 were determined in the collected samples. The connected functional landscape areas in the catchment supply the sedimentary material to the bottom sediments of the lakes. The decreasing order of concentrations of the elements in soils, surface-deposited sediments, and bottom sediments of water bodies was similar: Ti–Mn–Cr–Zn–V–Ni–Cu–Pb–Co–As–Sn. Such association confirms a similar genesis of metals in the lake and its catchment. Furthermore, the abnormally high salinity of snow-dirt sludge taken from the road is associated with the presence of an anti-ice mixture.