Navalny, a fierce Kremlin critic who says he will challenge President Vladimir Putin in next year's presidential elections, was detained at home by police as he was heading out to join Moscow's rally against what demonstrators call government-linked mass corruption.
Moscow police said Navalny would be charged with administrative offences of resisting arrest and a second violation of demonstration organisation rules.
Dozens of protesters were held in the centre of St Petersburg, and more than 50 of Mr Navalny's supporters were arrested by riot police near Pushkin Square in Moscow. "We left the Pushkinskaya metro station and after five minutes the riot police ran up to us and dragged us to the police bus, which after a few minutes was already crowded with people", the 18-year-old told CNN via text message.
Organizers in over 200 cities had filed requests to hold demonstrations Monday, out of which almost 120 were granted and 50 were rejected.
As police led the demonstrators to police vans, some of the protesters shouted, "Shame!", "Putin is a thief!" and "Freedom to Navalny!"
A rally in Novosibirsk, Russia's third-largest city that's nearly 3,000 kilometres east of the capital, brought out about 5,000 people, local organiser Sergey Boyko said on Navalny's YouTube broadcast. That was a key issue Monday for protesters, particularly his report on vast wealth allegedly acquired by Prime Minister Dmitry Medvedev.
"We are against the corruption that is costing the future of our young people", said Maria Badyrova, a protester in Moscow.
Those protests were the largest since a wave of anti-Kremlin demonstrations in 2012 and resulted in over 1,000 arrests, putting rare domestic pressure on Putin, who is expected to run for and win re-election next year.
The rallies were organized by vocal anti-Kremlin politician Aleksei Navalny and coincided with Russia Day, a national holiday, which helped to swell the crowds.
Navalny's wife, Yulia, reported news of his detention at his home in Moscow on his official Twitter feed.
The scale of the protests will show if Navalny can build on the success of a similar event in March, in which thousands took to the streets across Russian Federation.
"We are cancelling the rally on Sakharova (street) and relocating our very peaceful event to Tverskaya (street)", Navalny said.
The report, however, seems to have struck a nerve among some Russians, particularly the young, who participated in unusually large numbers in March's and Monday's protests.
In Moscow, thousands of angry protesters held an unsanctioned rally on Tverskaya, the capital's main street.
And the social-media team behind Mikhail Khodorkovsky, the founder of Open Russia, reported that a number of schools had threatened to expel students who attended the protests.
One of those arrested was the opposition leader, Alexei Navalny, who organised the protests and has since been jailed for 30 days. A contradictory figure, with ties to both the pro-democracy movement and Russian nationalists, Navalny made a name for himself with a series of explosive investigations into high-level corruption.
In this photo taken on Friday, June 9, 2017, Russian opposition leader Alexei Navalny gestures while speaking to people in the city of Perm, about 1200 kilometers (750 miles) east of Moscow, Russia.