According to the TASS news agency, water levels in the sewer rose quickly following a downpour and the victims were unable to escape to the surface.
The body of a man was later found in the Moskva river, TASS reported, after three others including that of a girl were discovered earlier in the day.
"He is the fourth person to have died after the tour through the underground sewers," a source in emergency services told TASS.
Video shared on social media showed investigators peering down a manhole cover in the capital, while divers searched the river Moskva.
Multiple tour guides offer trips down into the vast tunnels of the capital's sewer system, some of which were constructed during the 19th century.
One urban explorer said there were shelters in the tunnel where people could escape, but that nobody could be found.
"I hoped that maybe I would still be able to find some survivors there. There are two shelter points, but there was no one there," urban explorer Daniil Davydov told the RIA news agency.
Law enforcement have launched a criminal investigation into the organiser of the tour, local media said.
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