Lake Miccosukee forms the northern border between Jefferson and Leon Counties. Descriptions of Lake Miccosukee have varied over time, particularly in regard to coverage of the lake's surface with aquatic plants. Like Lake Lafayette, this was a "prairie lake." In 1876, a plant-clogged Lake Miccosukee was described as being "covered by maidencane, flag and bonnets with broad white flowers" (Rigby, 1876). Then, in 1914, considerable open water was noted, the lake was "covered with water to a depth of 2 to 5 feet and, toward the southern end, grass and button bushes project above the water" (Sellers, 1914). Aerial photographs taken in 1976, and again in 1988, depict a plant-clogged lake, only 19.4% of which was open water.

Aquatic plant cover has historically varied in Lake Miccosukee due to fluctuating water levels. In times past, this lake would drain and fill on what seems to be a ten-year cycle. The lake contains an active sinkhole in its northern extremity. This water in Miccosukee Sink represents the actual surface of the aquifer as the caverns beneath the sink reach into the aquifer. If a cup of water is poured into the surface of the sink, another cup of water enters the aquifer and the water level in the sink remains unchanged. At its southern end, the lake forms a connection with the St. Marks River, which once flowed overland from Lake Miccosukee, but now disappears underground until it resurfaces further south.

Over fifty years ago, before the sinkhole was walled off with earthen dikes to stabilize water levels, aquatic plant coverage of the lake's surface varied as the basin periodically emptied and refilled. When it refilled, most of the lake was open water. As aquatic vegetation grew back, more and more of the lake's surface gradually became covered with plant life. At the end of the 1990's, after 50 years of stabilized water levels, most of the lake was totally covered with aquatic plants and, as a contemporary description stated, "much of Lake Miccosukee was and is a marsh" (Cooksey, 1989).

In 1954, a control structure, complete with an earthen dike and a concrete spillway, was built around the sinkhole at the northern end of the lake to "keep the water in." At the southern end of the lake a wooden weir was built to keep the water from disappearing into Lloyd Sink. Between 1954 and 1988, the lake was stabilized to such an extent that the bottom was exposed only twice, in 1977 and 1988, for a total of 6 months (Cooksey, 1989). Water level stabilization accelerates the aging process of lake. The gate in this structure was opened in October 1999, and, during the drought of 1999, the lake was allowed to drain into the Miccosukee Sink into the Floridan Aquifer. The lake then went dry, except for its central valley, which remained full to preserve the fish population and the sink that retained water within its basin. Several areas of the lake were excavated and most of the lake bottom was burned during the drawdown. More extensive restoration could have created deep areas within the lake and future open water habitats, but permits could not be obtained form the Forestry Service to allow fires to burn the muck deposits within the lake. There was concern that smoke from the fires could cause traffic accidents on Highway 90 which crosses the lake system at its south end.

The fires promoted the growth of maidencane. Lake Miccosukee filled during hurricane season in the late summer of 2001 following tropical storms Allison and Barry, both of which dumped over 10 inches of rain on Leon County. After the lake refilled, the maidencane covered the lake bottom, rising above the water surface to give Lake Miccosukee the appearance of dry land. A hotter fire that burned down into the sediments might have suppressed the growth of this grass.

Stabilized marsh systems have poor sport fish populations, but offer good habitat for aquatic plants, waterfowl, and alligators (Cooksey, 1988). Alligator (Alligator mississippiensis) harvests on the lake net almost $30,000 annually. There is an estimated population of 1200 animals, though starvation and cannibalism reduce stocks after those periods when the lake drains.

Lake Miccosukee has some of the finest duck hunting in the entire area and is one of our truly scenic lakes. After the restoration work, the lake is full of juvenile fish that will provide excellent fishing. One endangered species of plant, the Miccosukee Gooseberry (Ribes echinellum) exists only in three localities in the world, two of which are on the shores of Lake Miccosukee. Situated as it is in an area that is sparsely populated, Lake Miccosukee is has excellent water quality and remains a natural retreat from city life.