Abstract <p>Microbiological and chemical-analytical studies of the quality of water and bottom sediments of the Amur River near Khabarovsk were carried out in different phases of water content. It was found that the water quality significantly depended on the water regime of the river and varied along the cross-sectional profile. During periods of a steady rise in the water level during freshets and inundations, the average number of all eco-trophic groups of bacteria was 3–6 times higher than during periods of water decline. The number of saprophytic bacteria at the rise in the water level and at the peak of the flood averaged ~3.5 thousand, heterotrophic—25.8 thousand, and hydrocarbon-oxidizing—0.8 thousand CFU/mL. At low levels, the deterioration of water quality was influenced by small rivers of Khabarovsk, which was reflected in the number of bacteria along the right bank 3–5 times higher than at the left. During the closed channel period and spring low water, methanol dominated in the volatile organic compounds in the water (up to 510 μg/L), which was recorded in 100% of the samples. Hexane (50%, up to 20.7 μg/L), <i>m</i>-xylene (50%, up to 6.5 μg/L), <i>o</i>-xylene (57%, up to 3.8 μg/L), and toluene (43%, up to 107.6 μg/L) were also frequently detected. During floods and inundations, the content of volatile organic compounds significantly decreased, but acetone (in 87% of samples) entered the aquatic environment from the flooded soils of the floodplains and vegetation—up to 55 μg/L at the peak of the flood. In the bottom sediments formed under the influence of the runoff of small rivers of Khabarovsk, accumulation of weakly decomposed organic matter is taking place: hydrocarbons up to 142&#xa0;mg/kg, volatile organic compounds up to 964.6 μg/dm³, and active production of organic matter is noted. In the bottom sediments formed under the influence of the runoff of the Songhua River, the concentration of volatile organic compounds was 2025.9 μg/dm³, and they were mainly of technogenic origin.</p>