The river has cut more deeply into its channel, lowering the water table across the floodplain. Riparian plant species have virtually disappeared and have been replaced by upland species. The g allery forests are gone. Scientists estimate that riparian habitat losses on the East Fork of the Gila are 95 percent or greater. Due to a lack of shade, the temperature of the river has increased to the point where Gila trout can no longer survive, and they have been replaced by warm-water species.
Water quality is poor due to high turbidity levels.
Many tributaries that once flowed year-round are now dry gravel washes. The Risk Unmanaged livestock grazing is responsible for the degradation of the upper Gila River and poses a serious, ongoing threat to the health of the river. Cows have been grazing the river banks for over 100 years. In the early 1950s, most stretches of the West and Middle Forks were taken out of grazing, although trespass cattle can still be found on the Middle Fork. The East Fork, however, continues to be grazed - in recent years, as many as 140 yearlings have been authorized during the winter season on one allotment.