The town is located on the banks of the river Ganges where it meets the river Koshi, thus making the town prone to flooding every year. Manihari is a small border town between the states of Bihar and Jharkhand. Sahebganj is the district town of Jharkhand which is 9 km from Manihari (nautical mile distance); there is regular ferry service. Chief Minister Nitish Kumar flagged off the first passenger train on the newly converted Broad gauge (BG) section of Katihar-Manihari in Katihar division of North-East Frontier Railway (NFR) at Katihar station. There are few local trains which run between Manihari and Katihar.