Police official Shailesh Thapa said 13 bodies have been recovered from the Seti river south of Mount Annapurna in Kaski district. Police were searching for dozens of missing people, including three Russian tourists who were trekking in the area, Thapa said. The names of the Russians were not immediately available.
The flooding reached the tourist resort town of Pokhara, about 200 kilometers (125 miles) west of Katmandu.
Thapa said the floods were apparently triggered by an avalanche on Annapurna.
Thousands of trekkers visit the Annapurna region each year. May is the end of the trekking season, so not many tourists were still in the area.
Many villages are located on the banks of the Seti river, which is a main source of water in the region.