The Indus River System is a major source of life in Pakistan. A vast array of Pakistan's agricultural and domestic consumption needs are critically dependent on the Indus River System. The Indus River contributes towards 25% of the country's gross domestic product, providing water for almost 90% of the food production in Pakistan. Linked to the water security issues, Pakistan is potentially at risk of facing a severe food shortage in the near future. The World Bank report of 2020–2021 estimates that the water shortage will increase to 32% by 2025, which will result in a food shortage of almost 70 million tons. Water shortage could also result in confrontation between the provinces as river sharing has always been a source of problem for Pakistan. According to recent estimates, siltation and climate change will reduce the water storage capacity by 2025 to almost 30%. As for the per capita water storage capacity in Pakistan, it is about 150 m3, which is quite meagre in comparison with that in other countries. Irrigated agriculture will soon be adversely affected due to the reduced surface water supplies and the consequent increase in groundwater abstraction. To make matters worse, over the past decades, a great deal of distrust has developed among the provinces of Pakistan regarding the water distribution issue, and the successive federal governments have failed to formulate a cohesive inter-provincial National Water Policy. Along with the shortages and increasing demand for water, administrative corruption also plagues the water sector and is quite common. The beneficiaries of this water reallocation system are not only the rural elite, for example the large and politically influential landlords, but also the small and medium capitalist farmers. If not properly addressed, these complications of decreasing water resources could result in serious political and economic hostility among the provinces. If it wants to harness its potential to increase storage capacity, Pakistan must improve its water-use efficiency and manage its groundwater and surface water resources in a sustainable way. Strengthening the institutions and removing mistrust among the provinces are the key elements for maintaining a sustainable irrigated agriculture in the Indus Basin.