Activists in Moscow pressed ahead with plans for a banned gig, after police confiscated their stage equipment.
The authorities say the concert, in protest against plans to build a motorway through the nearby Khimki Forest, was not authorised.
Yuri Shevchuk, the frontman of the popular rock band DDT, carried on regardless, singing acapella and strumming his guitar.
Opposition politician Boris Nemtsov, a vocal critic of Prime Minister Vladimir Putin, was later arrested while on an unauthorised march.
Flag Day in Russia is a public holiday and commemorates the day in 1991 when the Soviet-era red flag bearing the hammer and sickle was replaced by a white, blue and red tricolour over Government House in Moscow.
In St Petersburg participants came together to form a human flag.
The streets were a mass of white, blue and red.