The movement of marine transport vessels in Bangladesh waterways have become extremely slow and risky because of rising river beds from siltation. After the establishment of the Farakka Barrage in India during the mid seventies, the length of the waterways of Bangladesh shrank from 24,000 kilometres to some 7,000 kilometres. During winter, due to the lack of water flow the water level has shrunk drastically and siltation took its toll by reducing the total waterways to some 3,000 kilometres. This is a grave news for Bangladesh where water transport is one of the main (& affordable) mean of transporting goods and people. Lack of govt. budget will make it difficult to dredge huge areas of silted waterways. Read more here.
That is the reason why Bangladesh wants India to abandon its proposed river-linking project.