A review of topographical maps and flood plain maps reveals that mere apathy is enough to flood the southern half of Moscow and the western half of Leningrad/Petrograd/Saint Petersburg.
The Kremlin sits on a hill overlooking the Moscow River and rail yards are farther north, on higher ground. However the Moscow River is slow and shallow (3-6 metres) with numerous meanders and oxbows surrounded by swampy farmland. IOW for thousands of years, the Moscow River has gradually nibbled at the hill the Kremlin sits on. A clever hydrologist could accelerate the process and watch the Kremlin collapse into the river within his lifetime.
Merely rupturing dams - along the Moscow Volga Canal - would seasonally flood the southern half of Moscow .... everything south of the Kremlin.
Petrograd was built in a swampy River delta. Autumn storms have flooded the lower, western parts hundreds of times. Merely neglecting dams and drainage canals would allow Petrograd's low-lying western half to revert to tidal swamp.