After activists and ordinary Muscovites staged pickets last week, including outside the local election commission building, investigators said they were launching a criminal probe into obstructing the work of election officials.
If found guilty, organisers risk up to five years in prison.
Navalny ally Ivan Zhdanov said he had been arrested shortly ahead of the demonstration. Barred candidate Ilya Yashin meanwhile announced he was detained in the early hours of Saturday morning following a raid on his home.
Would-be candidate Lyubov Sobol, who this week launched a hunger strike, was arrested at the demonstration.
Moscow Mayor Sergei Sobyanin called the unauthorised protest a “security threat”, adding that “order will be ensured according to the relevant laws”.
Elena Rastovka, a 68-year-old pensioner at the demonstration, told AFP: “I’ve been afraid all my life, but enough is enough. If we stay at home, nothing will change.
“Authorities arrest people who want to challenge them. Look at what they’re doing – the authorities do not like the people.”
Some said it was the authorities’ heavy response that had turned a local issue into a major protest movement.
“Who would have thought it would become important to take part in such a bizarre and boring affair as the Moscow parliament election?” asked Viktoria Popova, a 30-year-old illustrator, ahead of the rally.