The continuous expansion of the irrigation system over the past century significantly altered the hydrological balance of the Indus River basin. Seepage from the system and percolation from irrigated fields caused the water table to rise, reaching crisis conditions for a substantial area. Around 1900 the water table was usually more than sixteen meters below the surface of the Indus Plain. A 1981 survey found the water table to be within about three meters of the surface in more than one-half the cropped area in Sindh and more than one-third the area in Punjab. In some locations, the water table is much closer to the surface. Cropping is seriously affected over a wide area by poor drainage--waterlogging--and by accumulated salts in the soil.

Although some drainage was installed before World War II, little attention was paid to the growing waterlogging and salinity problems. In 1959 a salinity control and reclamation project was started in a limited area, based on public tube wells, to draw down the water table and leach out accumulated salts near the surface, using groundwater for irrigation. By the early 1980s, some thirty such projects had been started that when completed would irrigate nearly 6.3 million hectares. By 1993 the government had installed around 15,000 tube wells. Private farmers, however, had installed over 200,000 mostly small tube wells, mainly for irrigation purposes but also to lower the water table. Private wells probably pumped more than five times as much water as public wells.

Officials were aware of the need for additional spending to prevent further deterioration of the existing situation. Emphasis in the 1980s and early 1990s was on rehabilitation and maintenance of existing canals and watercourses, ออออออon farm improvements on the farms themselves (including some land leveling to conserve water), and on drainage and salinity in priority areas. Emphasis was also placed on short-term projects, largely to improve the operation of the irrigation system in order to raise yields. Part of the funding would come from steady increases in water use fees the intention is gradually to raise water charges to cover operation and maintenance costs. Considerable time and money are needed to realize the full potential of the irrigation system and bring it up to modern standards.

Data as of April 1994