Rail lines in most parts of the district went under floodwater, halting service.
The district administration is currently using all educational institutions in the 13 Upazilas as shelters.
Four people drowned in the floodwaters between Sunday night and Monday morning, said Deputy Commissioner Khairul Alam.
Nine others died on Sunday.
Though buses, trucks and other large vehicles were able to use roads in the district, rail service was shut down on Sunday afternoon.
The Punarbhaba River water line is 80cm above the danger level, said Water Development Board Chief Engineer Faizar Rahman, but the water level has not risen since Sunday night.
Many areas of the district town, including Balubari Khalpara, Maldaha Potti, Chawkbazar, Neemtala, Mirzapur, Sheikhpura and the Eidgah slum area, are currently waterlogged.
According to local representatives, 12 wards of the Dinajpur municipality were flooded after the Punarbhaba River dam gave way and the Atrai River dam was breached.
All educational institutions in the area have been designated as shelters to help cope with the situation, DC Alam said.