Blue Hole was originally excavated as a limestone quarry, and crushed limestone from it was used to build many of the original roads on Big Pine Key. After it became part of the National Key Deer Refuge, it was replanted with native vegetation and allowed to return to a more natural state. The site offers a view into the geology and freshwater resources of the lower Florida Keys, where removing limestone exposed a freshwater lens within dense, non-porous limestone called Miami oolite. This lens forms when rainwater floats above underlying saltwater, and on larger islands such as Big Pine and No Name Key it supports diverse plant and animal communities and the distribution of pine rockland habitat. Over the past 100 years, sea level has risen about nine inches, and as it continues to rise, freshwater wetlands only three to six feet above sea level are expected to give way to brackish and saltwater habitats, affecting species that depend on freshwater, including south Florida slash pines, Key deer, Lower Keys marsh rabbits, and Lower Keys mud turtles. Blue Hole is not the only freshwater source in the lower Florida Keys, because hundreds of rain-filled freshwater wetlands occur throughout the Lower Keys, including solution holes, ponds, surface wetlands, and man-made mosquito ditches, and these vary seasonally between the rainy season from May through October and the dry season from November through April. Freshwater wetlands like Blue Hole attract wildlife including American alligators, usually a male and a female at this location, freshwater fish such as sunfish and mosquito fish, some exotic tropical fish, and several Atlantic tarpon that appeared after Hurricane Wilma in 2005 brought a five-foot saltwater storm surge over much of Big Pine Key. Birds found here include osprey, green heron, anhinga, magnificent frigatebirds, white-crowned pigeon, gray kingbird, white-eyed vireo, northern cardinal, migratory songbirds, and various hawks and falcons. The area also has illegally released exotic species, including tropical fish and non-native turtles, which can grow unchecked without natural predators and harm the ecosystem.