Fifteen thousand years ago, the climate was much cooler. Mammoth, mastodon, horses and bison roamed what was a grassy plain. Just to the left of the third fairway close to the green, the bones of a mastodon were found when the golf course was constructed in 1969. The University of South Carolina School of Archaeology excavated and found bones and artifacts at least 10,000 years old. As the Ice Age ended and the climate became warmer, mastodon and bison were replaced by deer and squirrel. What had been a vibrant stream running through the property became a calm brook. Prehistoric men, forming into tribes by that time, centered their life around it.

Two thousand years ago all of Snee Farm was controlled by the Seewee Indians who called it "Mock Lands", meaning our land. A thriving Indian city, Datah, was established on the brook which led to the Wando River. By the time the English arrived, the Seewee were allied with the Kiawah and Wando tribes. When the ship, Caroline, entered Bull's Bay in 1670, the Indians persuaded the captain to go on to what is now Charleston Landing. The Indians perhaps outwitted the English, who were thus placed between the Seewee and the fierce tribe of Westos to the south. A lively trade between the Seewee and English flourished due to the pottery and wood working skill of the Seewee.

In 1698, King William III of England granted the land which is now Snee Farm to Nathaniel Law, who in 1707, donated the land for Christ Church. The original property consisted of 1,100 acres and has changed size and owner many times over the years. In 1754, Colonel Charles Pinckney received the land, which is now part of the National Trust, from John Savage, as a fee for legal services. Some think Snee is evolved from the word fee. With the old English way of writing the letter F somewhat like the letter S, it is possible, but Colonel Pinckney also owned a Fee Farm at Ashepo. After building the present farm house, Colonel Pinckney settled into his abode, which was designed as a lawyer's retreat rather than a working plantation. When the British seized Charles Towne during the Revolution, Colonel Pinckney, under pressure, took an oath of loyalty to the crown. Subsequently, many prominent men captured by the British were paroled to Snee Farm, including Charles Coteswoth Pinckney and Colonel William Moultrie. One brief skirmish between the British and Patriots, possibly where the manor section is now, was the only actual fighting in the area. Because of the patriotism of son Charles, Snee Farm remained in the Pinckney's hands after the Revolution despite his father's oath in 1780. Many of those who had taken the oath were "relieved" of their property. When Colonel Pinckney died, son Charles was very famous nationally and served three terms as governor of the state. At the Constitutional Convention in Philadelphia in 1787, he presented what many called the "Embryo of the Constitution". The final document contained over thirty of his proposals.

In May 1791, George Washington ate breakfast with Governor Pinckney at Snee Farm under a huge oak (the stump still stands). The land was used in many different ways. Most of it was used for cotton and indigo. The lakes were created in the 20th century mostly for hunting and fishing. During the Civil War, the slaves of Snee Farm were recruited to supply labor for the defense works around Charleston. After the War, the South's plantation system was in ruins and Snee Farm suffered. But in 1935, Ann S. Ewing bought it for $15,000. She and her husband, the Canadian Ambassador to the Netherlands, began restoration. In 1966, the plantation was purchased by Snee Farm Golf Club and the house and adjoining grounds by Joyce and Guilds Hallowell. The Hallowells have continued restoration and in 1974 the house was designated a National Historic Landmark.