During this period, shallow draft steamboats were a frequent sight on Alachua Lake in the center of the prairie.

In 1970, the state of Florida acquired the land and has been in the process of restoring the environment to a more natural condition ever since.

[3] Before 1637, Francisco Menéndez Márquez, the royal treasurer of Spanish Florida, established the La Chua ranch in the vicinity of Paynes Prairie.

[4] The prairie became the stronghold of the Alachua band of the Seminole tribe under chief Ahaya the Cowkeeper by the mid-1700s.

The town and the surrounding prairie was named for the Cowkeeper's eldest surviving son, Payne.

Fort Tarver and Ford Crane were both located in Paynes Prairie during the Second Seminole War.

[7] After Indian Removal, the area became inhabited by European Americans, their slaves, and very small number of free people of color.

Then in late July and August 1891, the water levels of Alachua Lake suddenly dropped.

The subsequent urbanization of Gainesville increased the amount of stormwater directed into Sweetwater Branch and also pollutants.

[11] In 1975, the Florida Park Service temporarily restored half of the historic rate of flow of water from Newnans Lake to Paynes Prairie.

The project was designed to restore sheetflow to parts of the prairie obstructed by the Sweetwater Branch Canal and to also reduce the TMDL to acceptable levels that the Alachua Sink experiences.

The prairie itself is a large Floridian highlands freshwater marsh, composed of different herbaceous plant communities that vary based on water depth.

On drier uplands, southern coastal plain oak domes and hammocks of southern live oak (Quercus virginiana) grow in areas with moderately moist soils, and Florida longleaf pine sandhills grow on drier, sandier soils.

The plains bison were reintroduced to the park from the Wichita Mountains Wildlife Refuge in 1975, as part of the park service goal of restoring Florida's natural resources to pre-European settler conditions; they roamed this area until the late 18th century.

The park began culling excessive animals in 2012, allowing a target population of about 8 to 10 bison to be free to roam the Florida prairie.

[15][16][17] The park contains exhibits and an audio-visual program at the visitor center that explains the area's natural and cultural history.

[19] (Various sources stating that water entering the Alachua Sink flows to the Santa Fe River may be based on a story told by a Seminole guide to a white explorer in 1823, that a Seminole who had drowned in the sink was later found in the river.