The purpose of the barrage is to divert 1,800 cubic metres per second (64,000 cu ft/s) of water from the Ganges to the Hooghly River for flushing out sediment deposition from Kolkata harbour without the need of regular mechanical dredging.

After commissioning the project, it was found that the diverted water flow from the Farakka barrage was not adequate to flush the sediment from the river satisfactorily.

In addition, there are regular land/bank collapses in to the Ganga river due to the high level back waters of the Farakka barrage.

Substantial high land is already converted into low level river bed causing displacement of huge populations.

But after the assassination of Sheikh Mujibur Rahman on 15 August 1975, relations between the two countries became greatly strained and India continued to withdraw water even after the agreed period.

In Bangladesh, it is perceived that the diversion has raised salinity levels, contaminated fisheries, hindered navigation, and posed a threat to water quality and public health.

After the construction of the Farakka Barrage in West Bengal, the maximum flows in the Ganga-Padma River were reduced significantly.

The flow reduction caused many problems in India and Bangladesh, including the loss of fish species, the drying of Padma's distributaries, increased saltwater intrusion from the Bay of Bengal, and damage to the mangrove forests of the Sundarbans.