India and Pakistan are to attend a two-day meeting of the Permanent Indus Commission on Monday.
After a bilateral meeting between the Secretary Water and Power with the Indian Secretary for Water Resources, held in New Delhi in July 2016, both the disputed matters were referred for a third party resolution through the World Bank (WB).
The official statement appreciated India's decision to resume the regular talks and welcomed the Indian delegation to Islamabad.
The treaty which was signed in 1960 by Indian Prime Minister Jawaharlal Nehru and Pakistan President Ayub Khan gives India control over the three eastern rivers of the Indus basin, the Beas, the Ravi and the Sutlej while Pakistan has the three western rivers, the Indus, the Chenab and the Jhelum.
Sources said that Pakistan would highlight concerns about the three Indian hydro projects being built on the rivers flowing to Pakistan.
Mr Asif said the meeting would discuss the design aspects of Pakal Dul, Lower Kalnai and Miyar hydroelectric plants and flood data supply by India.
The treaty has been violated twice already when India constructed two hydroelectric power plants named "Kishenganga" and "Ratle" on the Neelum and Chenab rivers.
The Minister for Water and Power hailed the start of talks between Pakistan and India on the contentious issue of water, saying it is good for bilateral relations. He said that Pakistan had always been pleading that the Indus Basin Waters Treaty was one of the few world level treaties that provided forum to get resolution of water issues in a peaceful manner. Article IX deals with arbitration of disputes between both the countries concerning the interpretation or application of the treaty. The World Bank had brokered the agreement and have a role in dispute resolution.
India had suspended the annual PIC talks in Sept 2016 - ostensibly in wake of Uri attack in Occupied Kashmir.
Pakistan minister for water and power Khawaja Mohammed Asif reiterated on Monday that the Indus Waters Treaty (IWT) was an global agreement which provided an amicable solution to serious water issues between Pakistan and India. But there will be no compromise on India exploiting its due rights under the 57-year-old pact.
He further added that delays had been witnessed in the past in the handling of the Kishanganga project.