The deal to share Teesta river water was meant to be a highlight of Prime Minister Manmohan Singh's visit to Dhaka last September, but it fell through after opposition from the chief minister of India's West Bengal state.
The failure soured relations between India and Bangladesh, where Prime Minister Sheikh Hasina has staked much political capital in resolving an issue crucial for farmers in the country's drought-hit north.
"The Indian government is working on the Teesta deal. They are very sincere about it. So we are hopeful that it will be struck," Bangladesh Foreign Minister Dipu Moni told reporters after talks with Mukherjee.
Mukherjee on Sunday concluded a two-day visit to Bangladesh, where he met with Hasina to review agreements signed during Singh's visit, including one to end complex border territory disputes.
Bangladesh, formerly East Pakistan, won independence in 1971 with Indian military help, but relations have been patchy ever since due to decades of mutual mistrust.
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India should transfer all the land of Bengal to Bangladesh so it can complete Greater Bangladesh.
Mamts Banerjee should cooperate and Bangladesh should get a fair deal.