While turnout for the Russia Day demonstrations was said to be lower than mass protests in March, Navalny's influence was clear as protesters jostled with police and yelled anti-Putin messages.
Jill Dougherty, a Russia expert and former CNN Moscow bureau chief, said Navalny was likely to be plotting his next demonstration in the lead up to the presidential election next year.
"Right now he's thinking, 'what's next'.. In some way he's going to have a protest, but how and where is a tactical question. I'm sure he's looking for opportunities," she says. "(Holding Monday's protests) on Russia Day was definitely a tactical decision. He jumped on that."
The arrests topped detentions following similar, Navalny-led protests in March
. Then, as many as 700 protesters -- including Navalny -- were arrested, according to OVD.
Navalny is seeking candidacy in next year's presidential election -- something which, given his popularity amongst the country's youth, Putin would rather avoid.
His campaign comes despite him being convicted of embezzlement and given a suspended sentence in February. Russian laws prohibit convicted people from running for office. Navalny says the charges against him are politically motivated.
"According to Russian media, 70% of people at Monday's protest were in their teens or early 20s," says Dougherty, from the Evans School at the University of Washington.
"The Kremlin looks at these kids who are now maybe 17 or 18 and they know they're going to be voters in 2018, so they're trying to discourage them from support Navalny. There's a big outreach planned toward young people encouraging them that the government is on their side."
But Monday's protests and March's Navalny-organized anti-corruption demonstrations are evidence the government's grip on the political narrative is weakening, says one seasoned Kremlin-watcher.
"The significance of the event today, and the significance of the event at the end of March, is that the Kremlin is still making an impression that they control everything -- they set the rules, they set the boundaries, politics is monopolized by Putin, (and) they decide how it's going to develop," Arkady Ostrovsky, Russia and Eastern Europe editor for the Economist, told CNN's Christiane Amanpour.
He says the 41-year-old Navalny is "completely ignoring this rule, saying, you're fooling yourselves."
Ostrovsky says that while the Kremlin insists that they "control the rules and Navalny is saying, 'no you don't any longer -- look at these young people in the streets.'"
Those in their teens and early twenties at Monday's protest have never known anything but Putin's rule.
Teenager Anna Meigan said she was detained minutes after joining the protest in Moscow.
"My sister and I went to an anti-corruption rally. 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.
Ostrovsky says that Russia "often moves in generational shifts" and that Navalny is "well placed to exploit" the disenchantment of Russia's youth.
"These are 16-17 year old guys, and young women who basically need to understand what prospects await them in their lives and this is a very serious thing.
"This is a generational shift -- Russia has often moved in generational shifts -- and Navalny is very well placed to exploit and use that... these young people have clearly placed their faith in him; he's a clear political leader (in) the way he wasn't five years ago."
Widespread anger at a economy in the doldrums and perceived endemic corruption mobilized many to attend the street protests.
"We don't like his policies, a lot of my friends live below the poverty line, and then, there is the corruption," one young protester told CNN.
Corruption was also the rallying cry behind the day of protests in late March, also organized by Navalny. Anger at the problem goes deeper than criminal greed, says Ostrovsky.
"Corruption is much broader than just about finances, corruption is about the lack of values, corruption is about the moral vacuum."
Navalny is "brilliant" in the way he uses social media, says Dougherty, which is why he's so good at reaching young voters.
"He has a big sense of humor... he strikes a chord with young people, speaks their language, he has a big following on YouTube... that's one of the keys to his success."
The inherent democracy of the internet has left the Kremlin flat-footed, Sarkis Darbinyan, cyber law attorney and the head of Russian anti-online censorship NGO RosKomSvoboda, tells CNN.
Putin has left it too late to control the internet in the way he controls TV, he says. "In the beginning there was no control (and) no regulation.
"After 2012 they decided to make some control but technically they had no opportunity to make that control effective."
Moscow Conservatory student Daniil Pilchen made a name for himself online, mocking a list of supposed fifth columnists that he was required to read out in a mandatory class on cultural politics.
He said that young people were angry that the Kremlin was imposing its will on them.
"The government can't tell us what to do, what choices we should make, what music should we play," he said.
"When the government is invading culture it's always propaganda."