On March 3, 1857, Congress, for the third time, appropriated money for a lighthouse at Cape San Blas. This appropriation was for $20,000 and the new lighthouse was first lighted with a third-order lens on May 1, 1858.

The light station sustained serious damage at the hands of Southern troops during the Civil War. The keeper’s dwelling was completely destroyed and the door frames and sashes of the tower were torn or burnt out. Repairs were made, a new illuminating apparatus was provided, and the light was reexhibited on July 23, 1865.

In 1869 the beach in front of the lighthouse was reported to be washing away and would need protection against encroachments of the sea during heavy storms. In 1877 Congress appropriated $2,000 for protecting the site after the Lighthouse Board had reported 2 years earlier “The base of the tower is very nearly at the same level as the sea, which is but little more than 150 feet distant, the shore being of shifting sand. In a violent hurricane, it is feared, the tower may be undermined.” The Board had asked for $5,000 to protect the site and reported in 1879 that, as it was found “impracticable to build a jetty for $2,000 that can protect the site from the encroachment of the sea, no further action has been taken in the matter.”

Finally in 1881 the Board reported “The sea has been encroaching on this tower until its base is in the water. Brush mattresses were made, pinned down to the sand with small iron screw piles, covered with sand and occasionally blocks of concrete, to further check such encroachment, but the almost constant surf, beating against the mattresses, tore them to pieces. * * * An appropriation for a new tower, further inland is badly needed. It is recommended that a skeleton iron tower be erected; then if the sea again encroaches, it could be taken down and reerected. The new tower will cost $25,000.” The following year the Board noted “No appropriation was made; the site remained unprotected and on July 3, 1882, the tower was overthrown and completely destroyed.” The Board strongly recommended that the tower be replaced on a safe site at an early date, there being no intervening light between San Blas and Pensacola, 120 miles distant.

An appropriation for a fourth tower was made available in 1883. The remains of the third tower were then 400 feet distant from the shore, and the sea continued to erode the beach. By 1885 a fourth tower, a skeleton tower of iron, and two dwellings for keepers had been erected and the light was first displayed on June 30, 1885. The light had a third-order lens, showing alternate red and white flashes with 30 seconds intervals. The focal plane, 98 feet above sea level, lit the entire horizon.

In 1887 the sea was reported again gradually cutting away the shore and during the year had washed away about one-third the distance to where the new tower had been built (300 feet). Two years later only 200 feet of beach remained and the Board reported “It is more than probable that this will be mostly washed away in the next 4 months.” It was, therefore, recommended “that the tower and dwellings be taken down and removed to a point on the inside of the peninsula a little less than 1½ miles, about northwest from its present position where there is a good site and 8½ feet of water, in St. Joseph’s Bay, within 400 or 500 yards of it. This location is such that the bearing of the San Blas Shoals will be the same as now, and the increase of 1½ miles in the distance from the shore will be of little importance so far as its value as a coast light is concerned. It is estimated that to make the change will cost $20,000. The present site cannot be saved except at great cost.”

Nothing had been done, however, by Congress and by early 1890 the tower was only 144 feet from the sea at high water mark. Later that year, however, an appropriation of $20,000 was made to remove the tower and dwellings to the point inside the peninsula. Condemnation proceedings to obtain title to the new site, however, dragged on until 1894 when on October 8 and 9 a gale badly damaged the lighthouse extinguishing the light and wrecking the keeper’s dwelling. So much of the cape was washed away that the tower now stood in the water.

Before the tower could be removed to the new site, it was decided in 1895 to remove the station to Black’s Island, in St. Joseph’s Bay, which the President ordered reserved for lighthouse purposes. The work of dismantling the skeleton iron tower was begun in February 1896 and carried on until April 30 of that year when it was stopped because the appropriation was exhausted. The two keeper’s houses had been relocated on Black’s Island, the foundation for the tower was in place and three-fourths of the concrete work had been done, when it was estimated that $4,500 more would be required to finish the work. This was appropriated in June 1897.

Four months later, however, the light had been reestablished in the old tower, now in the water at the south point of Cape San Blas. In 1899 the Board reported “after careful consideration of all the conditions affecting the choice of a proper site, the Board has concluded that the light should be reconstructed on the shell ridge about 1⅜ miles N. by W. from its present location. It is estimated that this can be done at a cost not exceeding $15,000.” This sum was appropriated on June 6, 1900, at which time the Board reported: “that the property and material stored at Black’s Island was being cared for by a watchman appointed for the purpose.”