Navalny, who was barred from challenging Putin in March’s presidential election, had called on Russians to stage rallies across the country on May 5 under the slogan “Not our Tsar”.
Nearly 1,600 protesters were detained in 27 cities across Russia, according to OVD-Info, an independent monitor that tracks arrests.
Navalny was grabbed by police and carried away shortly after appearing in Moscow’s packed Pushkin Square.
The European Union condemned “police brutality and mass arrests” following the demonstrations, which saw officers in several cities beat protesters with truncheons and drag them along the ground.
Navalny has faced a string of charges since he became the leading opposition figure campaigning against Putin’s rule at mass demonstrations in 2011 and 2012.
He was jailed three times last year for breaking rules on organising demonstrations and had to travel to Spain for surgery after one of several street attacks left him nearly blind in one eye.