The capital Moscow was the runner-up in the study, presented on Friday and based on methodology developed by Ernst & Young.
Kaluga, a modern industrial hub 160 kilometers southwest from the capital, rounded up the top three, while Saransk and Izhevsk, both in the Volga federal district, closed the top five.
The city Tomsk in western Siberia was at the bottom of the list, with Tver in central Russia and Stavropol, a southern regional capital, also making the top three of Russian cities with the worst environment.
The list comprised 85 entries, but the bottom fifteen cities failed to provide sufficient information to determine their place in the ranking.
The rating was first compiled in 2011, when it was topped by another southern city, Volgograd, followed by St. Petersburg and Saransk. Kursk was fifth, Moscow sixth.
The study judged cities based on the quality of their air and water, recycling and energy saving effort, land use, traffic situation and environmental management.
Russia’s urban population stands at about 74 percent of the country’s total 143 million. The cities on the list are home to a combined 54 percent of the nation’s total population.