Protests in several cities were called by the Open Russia movement founded by arch-Putin foe and former oil magnate Mikhail Khodorkovsky.
They were held under the slogan "We're sick of him" - a reference to Putin.
About 200 people gathered in central Saint Petersburg for an unauthorised demonstration, an AFP journalist witnessed, and OVD-Info, which monitors detentions of political activists, said more than 110 protesters were hauled away by riot police.
"Police officers ended the actions... of 100 people who continued to trouble the public order," the Saint Petersburg police said, without confirming if they had been arrested.
"Putin is an usurper. He has to finally go. We're sick of him," said one of the protesters, 35-year-old Anton Danilov.
"Everything is bad. Education, health - everything has been destroyed. I want changes," said Galina Abramova, 57.
A similarly sized protest in Moscow remained peaceful as activists gathered at the offices of Putin's administration and handed in petitions against his expected candidacy in 2018.
"I don't want Putin to stand in the next elections," said Anna Bazarova, a 16-year-old student queuing up to hand in her petition.
Watch: Anti-Putin protestor confronts riot police
"Our main problem is that we can't change those in power," she said.
She added that many of her friends had opted not to attend, fearing detention by the police.
Riot police stood guard as officers used loudspeakers to warn protesters: "Citizens, your action has not been agreed by the authorities".
One of the organisers, Yakov Yermakov, handed out forms for people to fill out with complaints to Putin.
"Our president has already been in power 17 years. We think that's too long. Our country isn't developing," he said.
Will Putin run?
Putin has not tipped his hand on whether he will seek a fourth term as president in the election scheduled for March 2018.
The protests came after opposition leader Alexei Navalny organised the largest unauthorised rally of recent years in Moscow on March 26. Police detained around 1000 people, including Navalny.
Navalny has announced his plan to stand for president in 2018 and has galvanised the splintered opposition movement with a powerful online campaign including videos exposing corrupt officials. He has called for another protest on June 12.
On Thursday, Navalny was briefly hospitalised after an assailant threw green dye in his eye, causing a chemical burn which he said had damaged his cornea.
He had already been hit with green dye in a similar attack last month.
Khodorkovsky, the main figurehead of Saturday's protests, remains a controversial figure in Russia. The former oligarch and founder of the Yukos oil company spent a decade in prison and now lives in Britain.
His Open Russia movement has been targeted by the authorities recently with police raiding its Moscow offices this week, with the organisation saying the officers seized equipment and about 100,000 flyers for Saturday's protests.
