David Lilienthal, the former chairman of the Tennessee Valley Authority (TVA), visited the region and published his findings in Collier's magazine. He suggested that the dispute should be handled as a technical engineering challenge aimed at developing the basin as a whole. This 'Lilienthal Proposal' caught the attention of the World Bank president, Eugene Black, who then formally offered the bank's mediation services.

Professor Raymond Lafitte was the first Neutral Expert appointed under the IWT to resolve the Baglihar dispute. His 2007 determination upheld the dam's design for the most part but required India to reduce the height of the dam slightly. While both sides claimed a partial win, it demonstrated that the treaty's arbitration mechanisms could function even during periods of high tension.

On April 1, 1948, following the expiration of the Standstill Agreement, India cut off the water flow from the headworks in East Punjab to Pakistan's Central Bari Doab and Dipalpur canals. This crisis threatened Pakistan's agriculture and survival, leading both nations to realize that a technical and legal water-sharing framework was essential for regional peace.

The treaty allowed Pakistan a ten-year period (extended if needed) to construct a massive system of 'link canals' and storage dams. During this time, India continued to supply water from the Eastern rivers. This transition was supported by the Indus Basin Development Fund, which helped Pakistan re-engineer its entire irrigation network to become independent of the Eastern river flows.

The 850 MW Ratle project is a major point of contention. Pakistan has raised objections to its design, specifically regarding the storage capacity and the speed at which India can manipulate water levels. In 2023, the World Bank allowed the simultaneous processes of a Neutral Expert and a Court of Arbitration to address the Ratle and Kishanganga disputes, highlighting the increasing complexity of water diplomacy.

Per Article IX of the IWT, a 'Neutral Expert' is a highly qualified engineer or technical professional appointed to resolve technical differences. This mechanism was famously used in the Baglihar dispute, where Raymond Lafitte was appointed. The expert's role is to determine whether the technical design of a project (like gate elevations or pondage) conforms to the parameters allowed by the treaty.

The Permanent Indus Commission (PIC) consists of commissioners from both Pakistan and India. They are required to meet at least once a year, alternating between the two countries, to discuss technical designs of projects and exchange hydrological data. It serves as the first level of dispute resolution, aimed at settling 'questions' before they escalate into 'differences' or 'disputes'.

The project involves India's plan to build a navigation lock-and-control structure at the mouth of Wullar Lake on the Jhelum River. Pakistan contends that this is effectively a storage project, which is prohibited on the Western rivers under the IWT, while India maintains it is for maintaining water levels for navigation. Work on the project has been suspended for decades due to these unresolved differences.

The Kishanganga Hydroelectric Project involves the diversion of the Kishanganga (Neelum) river into another tributary. Pakistan argued that this diversion would severely impact its own Neelum-Jhelum Hydroelectric Project and agricultural needs in Azad Kashmir. The Permanent Court of Arbitration in The Hague gave a partial award in 2013, allowing the diversion but requiring a minimum environmental flow for Pakistan.

The Baglihar Dam is constructed on the Chenab River in Indian-administered Kashmir. Pakistan raised serious objections to its design, specifically the pondage and the placement of gates, fearing it would allow India to manipulate the flow of the river during critical farming seasons. The dispute eventually required the appointment of a Neutral Expert by the World Bank in 2005.