Thousands of people joined rallies nationwide, calling for the resignation of Prime Minister Dmitry Medvedev over corruption allegations.
At least 500 other protesters were detained in the capital and across the country.
Most of the marches were organised without official permission.
TV pictures showed demonstrators chanting "Down with [Russian President Vladimir] Putin!", "Russia without Putin!" and "Putin is a thief!".
Alexei Navalny was detained as he arrived to join the rally in central Moscow. Protesters then tried to prevent a police van from taking him away.
"Guys, I'm fine. No need to fight to get me out. Walk along Tverskaya [Moscow main street]. Our topic of the day is the fight against corruption," he said (in Russian).
He later said police stormed the office of his foundation and detained its staff, who were broadcasting the protests live.
Demonstrations were also held in Saint Petersburg, Vladivostok, Novosibirsk, Tomsk and several other cities, where arrests had also been reported.
The US has condemned "the detention of hundreds of peaceful protesters throughout Russia".
"Detaining peaceful protesters, human rights observers, and journalists is an affront to core democratic values," acting State Department spokesman Mark Toner said.
He added that the US was "troubled" by Mr Navalny's arrest.
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