The area surrounding Lyndon B. Johnson National Historical Park experiences storms that result in some of the highest rainfall rates in the United States. Generally the flood-producing storms that occur over the Pedernales River watershed happen in the spring and fall. The U.S. Geological Survey has two stream-gauging stations located on the Pedernales River near Fredericksburg and Johnson City. Stream characteristics for the Pedernales River at the LBJ Ranch District indicate that for the 100-year flood event, peak discharge would be at 220,200 cubic feet per second, 25 feet of rise above the bank at full stage, and a velocity in the channel of 21 feet per second (ArmyCorps of Engineers, 1979).

Due to the local topography and the hydrography (natural river flows) of the Pedernales River, large portions of land within both districts of the national historic park lie partially within the 100- and 500-year floodplains. In the LBJ Ranch District, several historic structures (both inhabited and uninhabited) lie within the 100-year floodplain, including the Junction School, the Reconstructed Birthplace, the Sam Ealy Johnson, Sr. Farmhouse, the Bailey House, and the Cedar Guest House. In addition, the Texas White House Complex is situated within the 500-year floodplain.