In addition to surface water, aquifers are an important source of freshwater in Central Asia. According to the FAO, total renewable groundwater resources are 6.1 km³/year in Kazakhstan, 13.69 km³/year in Kyrgyzstan, 6 km³/year (estimated) in Tajikistan, 0.36 km³/year in Turkmenistan, and 8.8 km³/year (estimated) in Uzbekistan. No data is available for Afghanistan. Groundwater is mainly used for the drinking water supply, but also for irrigation. In Turkmenistan, it counts for half of overall water consumption. Especially in the downstream areas of Amu Darya and Syr Darya, where surface water is scarce and polluted, groundwater is an important source of drinking water.

However, the quality of groundwater has also deteriorated over the last few decades. Ninety percent of Central Asian groundwater already has a natural salinity level of more than 1 g/l. Irrigation and drainage are the biggest sources of pollution. Several aquifers are reported to be contaminated by nitrogen substances, pesticides and hydrocarbons. Of minor influence is pollution from industry, mining and waste disposal, causing contamination by heavy metals, industrial organic compounds and radioactive elements. But in some aquifers, these have serious impacts on quality. The degradation of groundwater quality is especially serious in regions that depend on it for their drinking water supply, such as Khorezm and Karakalpakstan at the lower Amu Darya and Bukhara at the lower Zarafshan. In Uzbekistan, about 35% to 38% of the groundwater is not suitable for drinking anymore.

Most used groundwater is taken from aquifers that cross boundaries. The map below shows the locations of the transboundary aquifers identified by an UNECE assessment. Some are deep, with weak or medium links to local surface water systems that are recharged far from the border. Others are shallow and flow from neighbouring countries towards transboundary rivers. Though transboundary aquifers in Central Asia are large and have significant water resources, knowledge about them is still fragmentary and requires further research. To this day, no comprehensive legal and institutional regulation for transboundary groundwater is in place in Central Asia.[UNECE 2007, Rakmatullaer et al. 2010, MKUR 2006, FAO AQUASTAT]
Distribution of transboundary groundwater in Central Asia