In some areas, the extreme temperatures -- which in parts of Siberia dropped to minus 68 degrees Celsius (minus 90 Fahrenheit) -- the local authorities cancelled the rite which marks Epiphany.
Surrounded by Orthodox priests and glittering religious icons, and with the temperature hovering around minus 5 degrees C, Putin lowered himself into the freezing waters of Lake Seliger some 350 kilometres (220 miles) northwest of Moscow.
Many other Russians followed suit, submerging themselves in the freezing waters in a widely-observed ritual normally observed on 18-19 of January and which last year saw two million people take the plunge.
In Norilsk, a city beyond the Arctic Circle, local authorities on Thursday banned the extreme bathing rite "for security reasons" as temperatures hit minus 52 Celsius and strong winds whipped up a blizzard, RIA Novosti news agency reported.
Many faithful also marked the date in neighbouring Ukraine and Belarus, both of which are also predominantly Orthodox, local media said.
According to Orthodox tradition, worshippers are supposed to immerse themselves three times -- in the name of the Father, the Son and the Holy Spirit -- to remember the baptism of Jesus in the River Jordan. To mark the occasion, Orthodox priests also go out to bless rivers and reservoirs, and even bodies of water like the Black Sea and the Caspian Sea.