The Pedernales River is located in the LBJ Ranch District. Within the park there are two dams, the Jordan Dam and Johnson Dam, that impound water for use in irrigation of pastures. Erosion is severe in the Hill Country because of periodic heavy rains, thin soils, poor percolation, and severe runoff leading to incidents of extreme flooding.

The total Pedernales River drainage is 1,302 square miles; the area drained by the river before it reaches the park is approximately 602 square miles. The Pedernales River generally flows eastward through Gillespie and Blanco counties and drains into the Colorado River at Lake Travis in western Travis County, near Austin, Texas. From there the flows head southeasterly to the Gulf of Mexico. The Pedernales River is subject to severe flooding as well as very dry periods. The designated uses for the Pedernales River are contact recreation, high quality aquatic habitat, and public water supply.