Due to its location at the confluence of the Pho Chhu and Mo Chhu rivers in the Punakha-Wangdue valley, the Dzong is vulnerable to flash flooding caused by glacier lakes (GLOF). According to a recent report, flash flood damage to Punakha Dzong occurred in 1957, 1960 and 1994.
A covered wooden cantilever bridge crossing the Mo Chhu River was built together with the Dzong in the 17th century. This bridge was washed away by a flash flood in 1957 or 1958. In 2006 work started on a new covered wooden cantilever bridge of traditional construction with a free span of 55 meters which was completed in 2008.