The anthropogenic activities if not sensibly managed put enormous pressure on water resources of any country. Water quality of Kabul River has severely been polluted by rapid urbanization and industrialization. The sub lethal organic pollution is caused by discharge of effluents and other wastes into the river. The effluents from multiple leather processing units, and various other industries along with human feces and livestock manure are polluting the river ecology at an alarming rate. Climate is further impacting the quality of river and diminutive work has been done on climate change impacts on water quality. Integrated efforts are required to improve the water quality to reduce the morbidity and mortality rate in Pakistan and Afghanistan. In this review, water quality situation of Kabul River in Pakistan and Afghanistan along with potential impacts on health, agriculture and aquatic life under the changing climate scenario are presented. Water quality indices and modelling approaches for different parameters are suggested under the changing climate scenario which is expected to increase in the region to find the fate and transport of pollutants in the Kabul Rivers basin. Finally, recommendations were made to improve water quality of Kabul River and to decrease its adverse impacts.