Five river basins stretch over the territory of Afghanistan. Three of them cover the northern part of the country and are considered part of the Amu Darya Basin: The Panj-Amu Basin in the very northeastern area, the Haridud-Murghab Basin with the Murghab and Tejen rivers flowing into Turkmenistan, and the so-called Northern Basin, though its rivers still silt up on Afghan territory. Together, they cover about 37% of Afghanistan's territory and account for almost 50% of the total surface water availability in the country. The Panj, the Amu Darya's major tributary, forms the border of Afghanistan with Tajikistan. It is formed by the confluence of the Vakhan and Pamir Rivers. From the source of the Pamir, the Panj has a length of 1137 km. Important tributaries in Afghanistan are the Kunduz, the Koksha, and the rivers of Badakhshan.
There is limited data on how much water exactly is formed and used in the Afghan part of the basin, since the monitoring system broke down in the late 1970s due to the civil war. Based on previous data and recent studies, experts estimate that between 14 and 27% of the Amu Darya's flow is formed in Afghanistan and that it currently uses about 2 km³ (3%) of the average annual river discharge. Due to topography and climate, arable land is scarce and 94% of agriculture depends on irrigation. Consequently, agriculture is the main water user at 95%. The irrigated area in the Amu Darya Basin encompasses around 1.16 million ha (about 42% of the total irrigated area in the country), mainly subsistence agriculture, which most of the rural population of Northern Afghanistan relies on. Apart from that, there is a growing cultivation of poppy.
The agricultural sector's contribution to Afghanistan's GDP amounts to 33% (2008), but it absorbs about 60% of the labour force (2008). Therefore, the agricultural sector is considered important for the reconstruction and development of Afghanistan by the Afghan National Development Strategy and international donor agencies. Efforts toward reconstruction, poverty reduction and rural development include the rehabilitation of irrigation systems, re-cultivation of former irrigation land, and construction of small HPPs. All these efforts will increase water usage in Afghanistan, though not dramatically. In a study for the World Bank, Ahmad and Wasiq estimate that the technically feasible expansion and reconstruction of irrigation schemes would increase water use by 0.8 to 1 km³ per annum. A short-term increase beyond the levels of the 1980s seems unlikely. But under conditions of increasing water shortage in downstream areas, even a slight increase raises concerns.
Despite being an integral part of the basin, Afghanistan is not included in any regional agreements. Agreements between Russia and later the Soviet Union and Afghanistan on border rivers did not include provisions on water distribution. When the Soviet Union established the water limits for Syr Darya and Amu Darya, it did not consider Afghanistan, but only assumed that Afghanistan used 2.1 km³ of water annually. In addition, Afghanistan has not been involved in any regional institutions on water management since the Central Asian Republics gained their independence.[Ahmand and Wasiq 2004, CPHD 2011, FAO 2010, King and Sturtewagen 2010, AQUASTAT, WDI.]