Navalny, who organised the protest, was arrested by police after he arrived at the unsanctioned rally in the Russian capital on Saturday afternoon.
“Navalny appeared on Pushkinskaya [Square] and was quickly detained,” opposition politician Leonid Volkov said during an online broadcast.
Volkov called the detention “absolutely illegal”. Reporters with AFP news agency also reported Navalny’s detention.
Navalny, who has been jailed in the past for organising unauthorised protests, had called for people critical of Putin’s leadership to take to the streets in advance of the Russian president’s inauguration for a fourth term on Monday.
OVD-info, a human rights monitor, said about 1,600 people had been detained nationwide during widespread protests, including more than 700 in Moscow alone.
Arrests were made at rallies in 26 cities throughout Russia, including St Petersburg, according to the monitor.
Al Jazeera’s Rory Challands, reporting from Moscow, said it was difficult to tell exactly how many people had showed up at the protests due to different estimations from police and protesters themselves.
“But certainly this is a countrywide event that has brought thousands and thousands of Russians out on to the streets,” Challands said.
The demonstrations are intended to “keep the [opposition] momentum going”, Challands added, following Putin’s recent re-election to office in a ballot Navalny was prevented from entering.
Staunch Putin critic
Navalny, an anti-corruption activist and leader of the Progress Party, was barred from running in the March presidential elections after a Russian court reinstated a past criminal conviction for embezzlement.
The conviction had been previously overturned by the European Court of Human Rights, which ruled that Russia did not give Navalny a fair trial.
The European Union said the circumstances surrounding Navalny’s removal from the race cast “serious doubt” on the election.
Putin won the contest with 76 percent of the vote, his best ever showing.
Navalny has remained critical of Putin following the election results.
He tweeted on Friday that if people “stay at home, Putin’s gang will tear the country apart and deprive you personally of a future”.