The pollution of waters ecosystems is caused by natural and artificial factors in Tarim River. Temporal and spatial variation of surface runoff is the main reason for changes of coupling relationship between water and salt. In the end of 1950s, mineralization degree was less than 1.0 g.L-1 from the upper reaches to the lower reaches of Tetema Lake in Tarim River. At present, only in July, August and October, mineralization degree is less than 1.0 g.L-1. During the other months, mineralization degree is more than 3.0 g.L-1 in Alaer Lake. In Qiala (the lower reaches of Tarim River), mineralization degree is more than 1.0 g.L-1 except in March. Moreover, mineralization degree is about 5.0 g.L-1 in July and December. It is showed that annual water quality belongs to the fifth seriously polluted water in Alaer, Xinquman and Yingbazha. Meanwhile, annual water quality in Qiala belongs to the fourth polluted water. In a word, water quality state and hydrological chemistry component are the most obviously indicator for coupling relationship between water and salt in Tarim River.