Built in 1860 in order to fill a 35 kilometre dark space between the lights at Cape Pine and Dodding Head, as well as to aid the fishery in the area, the Cape St. Mary's Lighthouse was one originally of masonry construction. Although ready in 1858, repeated difficulties in reaching the site prevented the installation of the lantern until 1860.

In 1869, it was noted that the brick tower was deteriorating and was thus repointed and coated in cement. By 1883, this cement coating was also deteriorating, and thus the decision was made to encase the tower in an iron shell, much similar to what would later be done at Ferryland Head. 

The iron shell would support the structure until the 1950s, when it was again noted that the structure had once again deteriorated, with the iron rusting beyond repair. It was then decided to encase the tower in a third structural layer of reinforced concrete, giving it a bulky, octagonal shape. The light was later converted to electricity in the 1960s, and the original lighting apparatus was replaced by a modern system, producing a white flash every 5 seconds. 

Cape St. Mary's is also the site of an ecological reserve, with many different species of birds.