Mr Navalny himself is barred from running.
President Vladimir Putin is set to win, and is hoping for high turnout despite widespread apathy.
He is standing against 7 other candidates, including millionaire communist Pavel Grudinin and former reality TV host Ksenia Sobchak, but none are polling more than eight percent.
Mr Navalny was barred from the campaign because of a criminal conviction widely seen as politically motivated.
The Kremlin and election officials say any fraud will be stamped out.
Election monitors have already reported irregularities at voting stations across Russian Federation, just hours after polling stations opened. Britain and Russian Federation last week announced expulsions of diplomats over the spy case and the USA issued new sanctions. Only Russian diplomats were allowed to access official Russian premises. But the disputes likely worked in Mr Putin's favour, reinforcing the official contention that the West is infected with "Russophobia" and is determined to undermine Mr Putin and Russian cultural values.
Crimea and Russia's subsequent support of separatists in eastern Ukraine led to an array of U.S. and European sanctions that, along with falling oil prices, damaged the Russian economy and slashed the ruble's value by half. "That's Putin's main quality - he is at the core of our state".More news: Frustrated Trump lashes out at special counsel Mueller
In his next six years in office, Putin is likely to assert Russia's power overseas even more strongly.
Just weeks before the election, he announced that Russian Federation has developed advanced nuclear weapons capable of evading missile defences.
He is calling for a boycott of the election, saying it is an undemocratic farce, and deploying supporters to collect evidence of anyone rigging the ballot to inflate turnout and support for Putin.
"The programme that I propose for the country is the right one", he declared.
Given the lack of real competition in the presidential race, authorities had to struggle against voter apathy and in the process put many of Russia's almost 111 million voters under intense pressure to cast ballots.
Yevgeny, a 43-year-old mechanic voting in central Moscow, said he briefly wondered whether it was worth voting.
"We are a great big team together and I am a member of your team", he said, after a colorful show of high-energy musical performances.More news: Colts, Jets swap first round picks in 2018 National Football League draft
He spoke on condition of anonymity because he fears repercussions from his employers if he speaks publicly about the electoral pressure. A public service employee who asked to remain anonymous said that all the workers in his office were verbally told to go to a celebration rally commemorating the election on Sunday evening.
Authorities have pulled out all the stops to ensure a huge turnout, offering food discount vouchers and prizes for the best selfies taken at polling stations after a sexually-charged online campaign.
Sunday's election was the first presidential vote on the Crimean peninsula since Moscow annexed the territory from Ukraine in 2014, prompting a further decline in Russia's relations with the West.
By 1 p.m. on election day six years ago, a little over 30 per cent of voters had cast their ballot; in the capital itself, where turnout was usually lower than in other regions, figures showed a five per cent uptick in voting numbers compared to 2012 despite the unseasonably frigid temperatures, Efe reported.
Election commission chief Ella Pamfilova also said officials around the country are taking quick measures in response to claims of violations.
Putin, 65, cast his vote at a polling station in the headquarters of the Russian Academy of Sciences in Moscow's Lenin Avenue.
In Artyom, a man tossed several ballots into the box, according to Tatiana Gladkhikh, the head of the regional election commission. Navalny has called for a boycott of the vote.More news: Dancers describe how auto drove into nightclub
Sunday also marks exactly 4 years since Putin signed a treaty declaring Crimea part of Russian Federation following its annexation from Ukraine, an action that led to the war in the east of the former Soviet state. Ukrainian security forces blocked the Russian Embassy in Kiev and consulates elsewhere as the government protested against the voting in Crimea, whose annexation is still not internationally recognised. Ukraine is also angry over Russian support for separatists in eastern Ukraine, where a deadly conflict continues.
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