Authorities detained Navalny and more than 1,000 of his supporters on Monday, as they mounted demonstrations across the nation against government corruption.
The protests are the second mass action since March called by Navalny, who has announced his intention to run for president next year and has drawn a new generation to the streets through a relentless online campaign.
Thousands of Russians, many very young, chanted "Russia without Putin!" in the streets of dozens of cities.
The United States condemned the arrests, a rare criticism of human rights violations and the Kremlin from Donald Trump's administration.
White House spokesman Sean Spicer called "on the government of Russia to immediately release all peaceful protesters," detained in nationwide marches.
At least 770 people were detained in Moscow, where riot police tried to push the crowds back, sometimes by beating them with batons.
As riot police grabbed people and led them to police vans others demonstrators shouted "Shame!", "Putin is a thief!" and "Freedom to Navalny!"
Another 200 were arrested in Saint Petersburg, according to OVD-Info, an NGO that tracks arrests. OVD-Info had already reported more than 100 detentions in cities including Vladivostock, Kaliningrad, Norilsk and Sochi.
Navalny himself was picked up by police as he headed to the Moscow event.
Russian police officers detain a participant of an unauthorized opposition rally in Tverskaya street in central Moscow, 12 June 2017. Source: EPA
Thousands took to the streets in other cities across Russia, with the authorities sanctioning some gatherings and banning others. Some reports said authorities threatened university students with expulsion if they attended.
The 41-year-old Navalny's anti-corruption videos have needled the country's ruling elite and drawn crowds to the streets not seen since the protests against President Vladimir Putin's reelection for a third term in 2012.
'Mired in corruption'
Navalny, who plans to stand against Putin in presidential elections in March, appeared before a judge Monday evening. He faces up to 30 days in administrative custody for breaking rules on organising demonstrations, his lawyer said.
European Parliament President Antonio Tajani voiced his concern after Navalny's arrest. Rights group Amnesty International condemned "alarming scenes" of detentions and violence towards demonstrators, calling for their immediate release.
The recent rallies were galvanised by a film released by Navalny in early March, which accused Prime Minister Dmitry Medvedev of controlling vast personal wealth through a shadowy network of foundations. It has been viewed over 22 million times.
Russian police officers detain a participant of an unauthorized opposition rally in Tverskaya street in central Moscow, Russia, on Russia Day (AAP) Source: AAP
"Putin has been in power for 17 years and is not planning to leave. He has usurped all power," said protester Alexander Tyurin, 41.
Another protester Yevgeny, 19, said he had been expelled from university after participating in a previous rally.
"Our government shouts that enemies are everywhere and is becoming closed in on itself," he said.
"We want turnover among those in power. Pressure on young people has increased."
Navalny has brought a new generation to the streets through his embrace of YouTube. His team was broadcasting from a studio set up in Moscow, though the electricity was periodically cut, forcing the presenter to speak in total darkness.
Moscow police said Navalny would be charged with administrative offences of resisting arrest and a second violation of demonstration organisation rules.
Police detain a protester during anti corruption rally in St.Petersburg, Russia, Monday, June 12, 2017. (AAP) Source: AAP
Russia Day
The wave of protests called by Navalny coincides with a public holiday, Russia Day, when Putin hands out awards and holds a reception in the Kremlin.
Turnout was difficult to calculate as ordinary people mingled with those protesting, but thousands filled the Tverskaya Street area in Moscow, many waving Russian flags and banners.
On the eve of the event -- which was authorised -- Navalny announced the protest was changing location to Tverskaya because the authorities had blocked his efforts to set up a stage and sound equipment.
They "are forbidding any contractors from getting us a stage and sound," he wrote on his blog Sunday.
"We are cancelling the rally on Sakharov Avenue and moving it to Tverskaya Street," a main thoroughfare to the Kremlin, he said.
Moscow City Hall labelled the decision a "provocation" while the police warned that "any provocative actions by the protesters will be viewed as threat to public order and immediately thwarted".
The protest ended up coinciding with City Hall Russia Day events such as the reenactment of various eras in Russian history, from World War I trenches to a Renaissance fair and sword fighting.
In surreal scenes, dozens of buses filled by policemen were parked nearby ahead of the rally while ordinary people gawked at actors in period costumes.
Later, however, riot police and the national guard moved in, even on people sitting in nearby cafes, shouting "Go away! There is an unauthorised protest here!"
