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Fresh water was reported to be pouring out of Lake Worth through a small “inlet” into the ocean at a point about ten miles south of the Jupiter Inlet in 1866. The inlet tended to silt up, and had to be dug out again every few months. A new inlet was dug at a point north of the old inlet in 1877, where a rock formation called the Black Rocks would provide some protection for the inlet. Henry Flagler, a railroad magnate, had the inlet enlarged in 1894.

In 1915 the Florida Legislature chartered the Lake Worth Inlet District (which later became the Port of Palm Beach District). The site of the original inlet was chosen for the new inlet, which was completed in 1917. The new Lake Worth Inlet was improved several times over the next decade. The federal government assumed responsibility for the inlet in 1935, and continued to widen and deepen it and build up the jetties.

The inlet was dredged to a depth of 35 feet in 1967, and has been maintained at that depth ever since. There is a sand transfer system that pumps sand from the north side of the inlet to the south side to try to maintain the natural flow of sand southward along the coast.