Hundreds of the 41-year-old's supporters have gathered in the capital to rally against Mr Putin's regime, calling on voters to boycott what they believe will be a rigged presidential election on 18 March.
Mr Navalny, who has been barred from running in the election and whose office was raided by police on Sunday morning, urged his backers to continue to demonstrate despite being detained.
He said on Twitter: "This doesn't mean anything... you didn't come out for me, but for your future."
The outspoken politician could be charged with a public order violation, which may see him jailed for 20 days.
Reporting from Moscow's Pushkin Square, Sky News' Diplomatic Editor Dominic Waghorn said: "There's a lot of anger, a lot of frustration.
"People are telling us Putin's a thief, a gangster, that he needs to go to court. One person told us he's not doing anything for the country. They have had enough of him.
"There is a lack of direction and a lack of leadership, largely because the leaders have all been arrested on their way, but there is a lot of anger.
"It's worth noting that most Russians will not see any of this. The media here is state controlled so the only way to see this is by seeking out Alexei Navalny's YouTube channel."
Mr Navalny's YouTube channel broadcast footage of police arriving at the studio at his office on Sunday morning, which authorities said was a response to a "bomb threat".
One anchor, Dmitri Nizovtsev, was detained, along with Mr Navalny's Moscow coordinator Nicolai Lyaskin.
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Freezing weather conditions are thought to have had an impact on the turnout in Moscow, where there are thought to be somewhere between 1,000 and 2,000 protesters, but other demonstrations are taking place in other Russian cities, including Saint Petersburg and Vladivostok.
One protester there said: "They took these elections away from us they took away our votes. Our candidate was not allowed to run."
The OVD-Info group, which monitors political arrests, has reported scores of arrests in further cities, including Murmansk, Ufa and Kemerovo.
