Lake Woodruff NWR is located near the historic Ponce de Leon Springs State Park, which was named for the famed Spanish explorer who may have led Spanish forces through the area in 1513 in his quest for the Fountain of Youth. Development of this area dates back to when the Spaniards cleared a small area, planted it in sugar cane, and built a mill to process the cane.


Prior to Spanish exploration, this area was occupied by the Timucuan Indians and their predecessors dating back 8,000 years. Numerous Indian mounds and middens are located throughout the area. 


According to local sources, in 1804, William Williams moved from New Smyrna Beach to settle at Spring Garden, now known as DeLeon Springs, and was the first to raise corn and cotton. Farming operations occurred during the late 1800's on Tick Island, including an orange grove and cattle grazing. 


After Florida became a United States territory in 1821, Major Joseph Woodruff bought out Williams' 2,020 acre share of Spring Garden in 1823. The lake became know as Lake Woodruff and the refuge was later named accordingly. In 1952 a private land developer made an abortive attempt to develop about 3,000 acres east of Lake Woodruff for agriculture. Levees were constructed and two 2,400 gallons-per-minute pumps were installed to drain the land. This venture was found to be impractical and was abandoned. The pine timber was removed from Jones Island in 1957-58. Pine, cypress, and oak timber were removed from Tick and Dexter Islands before the federal government bought the land. Prior to acquisition, timber and shell removal operations occurred on Tick Island.


In 1964 the Service began purchasing land for the refuge. The Wilderness Act was established that same year. Additional land was incorporated into the area presently occupied by the refuge. Lake Woodruff NWR was established in 1964 as a migratory bird refuge to offset losses of wetland habitat in central Florida.