At the 2000 Summer Olympics in Sydney, Nachaev competed as a member of the Uzbekistan team in the 4×100 m freestyle relay, along with Oleg Tsvetkovskiy, Petr Vasiliev, and Oleg Pukhnatiy. Although he swam the anchor leg in heat one, his team had been disqualified due to an early relay takeoff by Pukhnatiy. On the sixth day of the Games, Nachaev swam his two individual events, with only 90 minutes in between. First, he posted a lifetime best of 23.12 to lead the fifth heat of the 50 m freestyle. More than an hour later, in the 100 m butterfly, Nachaev stormed the entire field to another triumph in heat three by 0.04 seconds, with a time of 55.21. Despite winning the heats in just a single day, he failed to advance into the semifinals in any of his individual events, finishing thirtieth in the 50 m freestyle, and thirty-fourth in the 100 m butterfly.