Saturday's protests took on an unprecedented geographic scale, spanning more than 100 cities across the country. Previous large-scale opposition demonstrations in 2012 and 2019 were largely centralised in Moscow.
They were also being seen as a test of the opposition's ability to mobilise ahead of parliamentary elections later this year, despite increasing Kremlin pressure on critics.
In Moscow, protesters spilled out over Pushkin Square and pelted heavily armed riot police with snowballs. They were beaten back by law enforcement wielding batons and detained in large numbers.
The demonstrators marched towards the Kremlin before dispersing, and at one point massed on the steps of Moscow's circus, illuminating the crowds with hundreds of cell phone lights and pummelling a police van with snowballs.
"Criminals dressed in uniforms are protecting criminals at the helm," Vera Spivakova, a 71-year-old pensioner, told AFP in Moscow.
"Putin and the oligarchs are afraid of losing their trough," she said.
OVD Info, which monitors opposition rallies, said on Sunday that police seized at least 3,324 demonstrators across dozens of cities, with 1,320 people detained in Moscow and 490 in the second city Saint Petersburg.
It was the largest number of detentions at opposition rallies in the history of modern Russia.
The European Union's Mr Borrell said he deplored "widespread arrests" and the "disproportionate use of force".
Meanwhile US State Department spokesman Ned Price said Washington "strongly condemns the use of harsh tactics against protesters and journalists".
Mr Navalny being taken into custody and the arrests of his supporters were "troubling indications of further restrictions on civil society and fundamental freedoms," he added.
Canada also voiced "deep concern" and urged Moscow to "immediately release" those detained.
On placards and in chants, protesters referenced an investigation published this week by Mr Navalny into an opulent Black Sea property allegedly owned by Mr Putin. The two-hour report has been viewed more than 75 million times on YouTube.
Later Saturday hundreds gathered outside Moscow's high-security prison where Mr Navalny is being held but were pushed back by police.
Leonid Volkov, who heads Mr Navalny's regional network, estimated that as many as 300,000 people had joined the "unprecedented" nationwide protests, and called for fresh rallies next weekend.
The Investigative Committee, which probes major crimes, said in a statement it had launched several preliminary probes into violence against law enforcement.
Meanwhile, prosecutors in St Petersburg said in a statement late Saturday that they were probing violations including "on the part of law enforcement" and the use of force against an unidentified woman.
AFP journalists, who saw badly injured protesters retreating behind other demonstrators after clashing with police, estimated crowds in Moscow at around 20,000 people, with more than 10,000 in second city Saint Petersburg.
Mr Navalny's detention drew sharp condemnation from Western countries, and the US embassy in Moscow Saturday accused Russian authorities of "suppressing" the right of demonstrators to peaceful protest.
Moscow hit back by alleging US diplomats had published protest routes in advance of Saturday's demonstrations and of promoting a "march on the Kremlin".
"Senior officials in the US embassy will have to have a serious conversation with the Russian foreign ministry," it said in a statement.
'Tired of Putin'
Earlier Saturday thousands took to the streets in the Far East, Siberia and the Urals including Khabarovsk, Novosibirsk and Yekaterinburg, despite sub zero temperatures and police warnings of a swift crackdown.
In Saint Petersburg, 20-year-old Alexei Skvortsov told AFP that he no longer wanted to live in a "dictatorship".
"People are tired of Putin," he said.
In Yakutsk south of the Arctic Circle, protesters wrapped up against the cold and rallied in temperatures of minus 50 degrees Celsius.
Russia's media watchdog warned online platforms against encouraging minors to participate in the rallies or risk hefty fines.
A hastily organised court on Monday jailed Mr Navalny for 30 days for allegedly flouting parole conditions.
The 44-year-old trained lawyer rose to prominence a decade ago, leading large-scale street protests against corruption and electoral fraud.