Thousands of people joined rallies nationwide, calling for the resignation of PM Dmitry Medvedev over corruption allegations.
At least 500 other protesters were detained in Moscow and across Russia.
Most of the marches were illegal, organized without official permission.
TV footages showed demonstrators chanting “Down with [Vladimir] Putin!”, “Russia without Putin!” and “Putin is a thief!”.
Correspondents say the marches appear to be the biggest since anti-government demonstrations in 2011 and 2012.
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.
In a tweet after his detention, Alexei Navalny urged fellow protesters to continue with the demonstration.
He said: “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.”
Alexei Navalny 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.
In Moscow, protesters filled Pushkin square and some climbed the monument to poet Alexander Pushkin shouting “impeachment”. Turnout was estimated to be between 7,000 and 8,000, according to police.
The police said 500 protesters had been arrested in the capital alone, but a rights group, OVD Info, put that number at least 700.
The Kremlin has not commented on the demonstrations. It had said on Friday that plans for an unauthorized protest in central Moscow were an illegal provocation.
State TV channels did not cover the demonstrations.
Local media reports suggested the authorities pressured students not to attend. In some cities, exams were scheduled on March 26.
Alexei Navalny announced his intention to run for president in 2018 against Vladimir Putin.
However, he is barred from doing so after being found guilty in a case he said was politicized.
Alexei Navalny said on his website that protests were planned in 99 cities, but that in 72 of them authorities did not give permission.
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