The Pedernales River is subject to frequent flooding. When these floods occur the river's turbulence erodes the bottom and sides of the river channel, transporting soil downstream. River erosion and the shifting of river channels are natural phenomena. Cultural practices such as the removal of riparian vegetation to create pastures or the watering of stock animals along the riverbank can increase riverbank erosion. The impoundment of water behind dams can also disrupt the flow of sediment downstream and starve the riverbanks of soil replenishment. Dams also increase the river turbulence in the area of the dam. Along the stretch of the Pedernales River near the LBJ Ranch, three dams were built in the river to provide water for crop irrigation and to impound water for scenic views. Riverbank erosion is compounded by the presence of nutria, an exotic rodent species. Their burrowing activity serves to weaken the riverbank and make it less resistant to erosive flood waters.

In 2002, the National Park Service began to exclude cattle from the riverbank, allowing riparian vegetation to regrow along the channel in an attempt to stabilize the bank. The park is currently seeking further scientific analysis of the hydrologic activity in the Pedernales River in order to better preserve the natural and cultural resources at the LBJ Ranch.