In Moscow, where the authorities had rejected an application from Navalny's supporters to protest, around 2,000 people gathered in the central Pushkin Square, the authorities and Reuters reporters estimated.
Government plans to raise the state pension age to 60 for women and 65 for men, from the current 55 and 60, have also seen Putin's approval ratings take a major hit.
The OVD-Info group, which tracks police detentions and posts the names of the detainees on its website, said Monday that 1,018 people were detained, almost half of them in St. Petersburg.
The changes, going through parliament, have shaved around 15 percentage points off President Vladimir Putin's popularity and are the most unpopular government measure since a 2005 move to scrap Soviet-eras benefits, which led to nationwide pensioner protests.
The rallies were announced last month by opposition politician Aleksei Navalny, who is now serving a 30-day jail sentence for what authorities call violations of the law on public gatherings related to street rallies in January.
After an immediate backlash from the public, Putin agreed to decrease the new retirement age for women to 60.
SpaceX launch planned for late Sunday night
The recovery of this expensive part of the rocket is needed for SpaceX to achieve its dream of reducing launch costs. SpaceX's Falcon 9 launched early Monday morning, carrying a powerful telecommunications satellite into orbit.
YouTube has taken down a Russian opposition politician's YouTube ads after an official request. But some of the protesters started marching toward the Kremlin before riot police halted them with metal barriers and sometimes rough detentions.
"These elections are a defeat for the authorities", said Valery Solovei, a political analyst at the Moscow State Institute for International Relations. Photos and video footage from St. Petersburg show the police violently beating protesters.
A lawyer for Navalny's Anti-Corruption Fund was arrested in Moscow before the rally. Protests organised by the Communist Party were held across Russian Federation earlier this month.
Raising the pension is opposed both by older people, who fear they will not live long enough to collect significant benefits, and by younger Russians anxious that keeping people in the workforce longer will limit their own employment opportunities.
Pension reforms have caused widespread public anger, and Mr Navalny's supporters have planned rallies in more than 80 cities to capitalise on this.
Navalny's group said its St. Petersburg coordinator and another of its activists were detained in St. Petersburg as well.
The World Health Organization says in 2016, the life expectancy of a Russian man was 66.