Lyndon B. Johnson National Historical Park has been engaged in water quality monitoring at two sites on the Pedernales River since 1996. The monitoring was initiated in response to park concerns related to nutrient and bacterial contamination from livestock grazing on lands upstream from the ranch. The monitoring is conducted by park staff as part of the Colorado River Watch Network, which is sponsored by the Lower Colorado River Authority (LCRA). Water quality measurements are taken once a month for the following parameters: water temperature, pH, dissolved oxygen, total dissolved solids, nitrate nitrogen, phosphates, and fecal coliform bacteria.

Other water quality monitoring efforts in the park have addressed potential effects on drinking water wells from pesticide treatment of the nearby pecan grove.