Two bodies, including that of a teenage girl, were reportedly found over Sunday night in the Moskva River in the central city, near the Zaryadye park.
The tourists had been prevented from reaching the surface by flooded tunnels, according to rescue workers quoted by Tass.
Reuters quoted another local news agency that claimed as many as eight tourists may have been involved.
Tour guides and “urban explorers” had been involved in the rescue operation, saying there were areas where tourists could still be safe.
“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.
The agency also reported as many as 12 guests cancelled at the last minute after seeing the forecast for rain.
So far the known victims have been identified as a man and his 15-year-old daughter and 17-year-old nephew who had been on the tour. Tributes continue on Russian social media.
The city’s historic sewers, which date back to the 1800s, are the site of several tour operations leading tours into Moscow’s underground history.
Charging between $70 and $200, tours take visitors to visit underground waterfalls and the historic Moscow dungeons, but most advise that trips will be postponed or cancelled in case of rain.