The light stands on the southern side of the entrance to Charleston Harbor, north of the City of Folly Beach.

However, the construction in 1889 of the jetties which protect the shipping lanes leading to Charleston Harbor altered ocean currents, resulting in the rapid erosion of Morris Island and the destruction of many structures and historical sites (such as Fort Wagner).

Early in January 1861, the Rattlesnake Shoal Lightship was towed into Charleston and the lighthouse tenders were seized.

In 1865 the Lighthouse Board reported "that an almost total change had taken place, leaving no channel in the harbor as it was in 1860, and opening new ones.

Under this altered state of things it became necessary to establish lights temporarily at such places as would be useful guides through existing channels and omit all other.

$60,000 was granted on that date for "commencing the rebuilding of a first-order seacoast light on Morris Island destroyed during the war."

The cyclone (hurricane) of August 25, 1885, destroyed the rear beacon of the Morris Island range, overturned part of the brick wall which enclosed the tower and dwelling of the main light, carried away the bridge between the beacons, and destroyed a large part of the plank walks connecting the several lights and dwellings, and overturned the boathouse.

The 1886 Charleston earthquake threw the lens of the main light out of position and cracked the tower extensively in two places, but not so as to endanger its stability.

[citation needed] Erosion of land caused the Coast Guard to begin construction of a new Charleston Light in 1960.

The tower stands 140 feet (43 m) high on the north side of Charleston Harbor entrance on Sullivan's Island.

The lighthouse was leased to Save The Light, Inc. for 99 years to coordinate the stabilization, erosion control, restoration and to raise the necessary funds for that work.