Thousands of people have joined rallies nationwide, calling for the resignation of Prime Minister Dmitry Medvedev over corruption allegations.
Most of the marches have not been authorised by the authorities.
Police have been deployed in large numbers in Moscow where dozens of other protesters have also been detained.
TV pictures showed demonstrators chanting "Down with Putin!", "Russia without Putin!" and "Putin is a thief!".
Mr 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, he urged fellow protesters to continue with the demonstration.
"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).
Protesters block the bus where Alexei Navalny was kept
A rights group, OVD Info, said at least 130 people had been detained in Moscow and that police had used pepper spray to disperse the crowd, AFP news agency reports.
Alexei Navalny called for the nationwide protests after he published reports claiming that Mr Medvedev controlled mansions, yachts and vineyards through a shadowy network of non-profit organisations.
The prime minister has not commented on the claims.
Demonstrations were also held in Saint-Petersburg, Vladivostok, Novosibirsk, Tomsk and several other cities, where arrests had also been reported.
Between 3,000 and 4,000 protesters have gathered in Moscow, reports say
Dozens of protesters have been arrested in the capital
Mr Navalny announced his intention to run for president against Vladimir Putin in 2018. But he is barred from doing so after being found guilty in a case he said was politicised.
He said on his website that protests were planned in 99 cities, but that in 72 of them authorities did not give permission.