The Banteay Meanchey city jail was flooded with more than 18 inches of water Saturday when the Serei Sophorn River overran its banks, The Phnom Penh Post reported Tuesday.
The prison, which holds 1,000 people including 10 children, is 50 percent over capacity, a recent report by human rights organization Licadho stated.
Mass evacuation of the prison would be a "logistical nightmare," said Adam Hutchison, director of Prison Fellowship Cambodia.
It has never been done because it would be a security risk, said Marie-Dominique Parent with the United Nations' human rights office in Cambodia.
Banteay Meanchey's jail was built on a flood plain, said Jeff Vize, prison project consultant with Licadho. The facility has been flooded three times in the three years since it was built.
Floods in September 2011 left Siem Reap prison with more than 3 feet of water.