People remained on the streets as night began to fall, as a number of small scuffles with police officers - who earlier in the day had appeared relaxed about the protesters - were recorded by reporters following the marches.
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. That has been the strength of Alexei Navalny, the only credible opponent to President Putin.
Supporters of Alexei Navalny fill Pushkin Square in central Moscow.
Navalny warned that authorities planned to clamp down on his youngest supporters, tweeting a screenshot of a text message sent around ahead of the rallies.
Moscow Police said Navalny was taken to a police station for arraignment and to be charged for illegally organizing a protest, according to CNN.
Authorities have refused to grant permission for rallies in Moscow and St Petersburg, raising the prospect of mass arrests. Other unsanctioned rallies took place in Vladivostok, Murmansk, Kaliningrad, Volgograd and elsewhere.
The rally was among protests nationwide in support of opposition leader Alexei Navalny's call to boycott the March 18 presidential election.
Police also detained several employees of his Anti-Corruption Foundation as well as supporters, Navalny's team said.
Protesters also turned out in arctic areas of the country, where the temperature during winter is around -40 degrees, said CNN's Fred Pleitgen in Moscow. "Go out to the demo in your city".
Mr. Navalny posted on Twitter a photograph of police taking a saw to the door of his headquarters in order to interrupt a live webcast describing events around the country.
A video stream on Sunday morning from the opposition leader's headquarters showed police entering the office. In polar Murmansk, just a handful of people milled about under a giant New Year's tree while children played nearby.
Navalny has denied wrongdoing and condemned the charges as trumped up to thwart his political ambitions.
The Kremlin has rejected allegations of widespread, high-level corruption and has condemned Navalny as a risky influence whose calls for protests could plunge Russian Federation into chaos.