Many of the rarest species and most precious ecosystems are protected in eight nature reserves (zapovedniks), which cover desert, mountain, coastal and riparian environments. But the nature of Turkmenistan faces considerable challenges. Hunters threaten rare species such as the leopard. In the Caspian, the arrival of the comb jelly, mnemiopsis, probably carried in on the hulls of ships, threatens the slocks of indigenous fish by devouring the plankton on which the fish feed. The major environmental challenge facing arid Turkmenistan, however, remains, as it always has been, the sustainable use of water.
Agriculture in Turkmenistan is almost entirely dependent on irrigation. The control and management of water resources has long been crucial to human settlementin the area. The focus in the Soviet period on cotton ('white gold') involved a large expansion in areas under irrigation. In the post-independence period, to cotton has been added a major drive to achieve self-sufficiency in wheat production, and these two state-order crops dominate Turkmenistan's irrigated lands. The government increases its production targets for both cotton and wheat every year, adding to the pressures to bring more land under irrigation and to increase yields through more intensive farming. More than 90% of irrigation waters in Turkmenistan are taken from the Amu Darya River, under an agreement with Uzbekistan, especially through the Kara Kum Canal. This heavy off-take take from the Amu Darya has been one of the contributory factors in the gradual drying up of the Aral Sea, an environmental problem with significant regional consequences.
The main method of irrigation used is traditional surface irrigation. Over-watering is endemic. Coupled with often inadequate drainage, this has led to rising water tables and soil salinisation as salts are drawn to the surface. Abandoned fields, covered by a white dusting of salt, are a common sight across Turkmenistan,, especially in Dashoguz Region. Water is taken off the fields by a network of drainage channels , feeding large 'collectors' whose waters form the input for artificial bodies of water such as Lake Sarygamysh. These waters are often highly polluted. Large quantities of inorganic fertilisers have been used since Soviet times to try to generate high yields on Turkmenistan's poor desert soils. And herbicides are widely applied to defoliate cotton plants to make the cotton easier to harvest, especially mechanically.