The 41-year-old opposition politician has called on Russians across the country to defy authorities and stage rallies calling for an active boycott of Russian presidential elections in March, despite the prospect of mass arrests.
A tweet from his account read: "I've been detained. Come to Tverskaya. You're not coming out for me, but for your future", the post said.
Rallies were planned across 100 Russian cities, including St Petersberg, Vladivostok, Yekaterinburg - Russia's fourth largest city, and remote cities like Murmansk.
Police officers told those present that they were acting on a tip-off about a potential bomb threat, organisation officials said.
The anticorruption crusader took to Twitter to announce that he had been detained after joining a rally of more than 1,000 people in central Moscow.
Footage of his arrest was quickly shared on social media, as Navalny urged people to continue to turn out and march against president Vladimir Putin.
"To be honest, I don't support especially Navalny", Pavel Tikhonov, a 29-year-old who works for an global company, tells NPR's Kim. "That's what we came here to say".
Sizable gatherings, from a few dozen to several hundred, reportedly cropped up around Russian Federation after Navalny called for protests.
George Soros Just Launched A Scathing Attack On Google And Facebook
Furthermore, the magnate has also taken aim at tech giants, namely advocating stricter regulation for Google and Facebook . The billionaire investor said these technology giants are not mere distributors of information as they claim to be.
Footage taken by Mr Navalny's organisation showed nearly a dozen police officers arriving at his Moscow office on Sunday morning and breaking down the door, before entering the studio and interrupting a live broadcast.
Putin won the previous election in 2012 on a turnout of 65 percent and authorities are pulling out all the stops to boost the figures this year.
Fourteen people were arrested at a rally in Kemerovo, a city in western Siberia. Police in Nizhny Novgorod put turnout there at 550, according to the RIA Novosti news agency.
The United States and the European Union criticised the decision.
Moscow Police said Navalny was taken to a police station for arraignment and to be charged for illegally organizing a protest, according to CNN.
Ahead of the Moscow rally police broke into Navalny's headquarters using a power saw, interrupting a live broadcast covering protests in the east of the country.
As the crowd swelled to a few thousand people, hundreds of police armed with batons and many wearing riot helmets lined the streets leading to the Kremlin.
