The St. Marks and Wakulla rivers are critical to the Apalachee region's ecosystem and central to the areas wealth of outdoor recreation. In fact, these rivers' health is so important to the region that they were the subject of a special study by 1000 Friends of Florida and the Northwest Florida Water Management District entitled St. Marks and Wakulla Rivers Resource Assessment and Greenway Protection Plan.

The St. Marks River originates in the hardwood and cypress river swamps of the Red Hills area and flows for 35 miles through Florida before emptying into Apalachee Bay. At Natural Bridge, it disappears underground and reappears a mile downstream. Its major tributary, the Wakulla River, is one of the few spring-fed rivers in northern Florida. The Wakulla River rises from Wakulla Springs and the Floridan Aquifer at Edward Ball Wakulla Springs State Park, then flows south for ten miles to its confluence with the St. Marks River at the town of St. Marks. These two rivers generally have good or excellent water quality, and both have been designated as Outstanding Florida Waters except for the portion of the St. Marks River adjacent to the industrial complex of the town of St. Marks.

Numerous sinks and streams disappear into the ground north and west of Wakulla Springs, and it is widely speculated that there is a strong relationship between surface waters entering the sinks to the north and outflow from the Springs. This was borne out when abnormally heavy rains in 1994 turned the normally clear spring waters dark with tannin from surface waters.

The St. Marks and Wakulla rivers are lined with hardwood and cypress swamps for much of their lengths. Near their confluence, river swamps gradually give way to freshwater tidal swamps and salt marshes. Most recreational opportunities in the watershed are closely linked to the natural features and beauty of these two rivers. The watershed includes sites that draw visitors to the outdoors for fishing, hunting, hiking, swimming, horseback riding, off-road bicycling, in-line skating, canoeing, and manatee watching. These include Wakulla Springs State Park, popular for picnicking, swimming, snorkeling, hiking and boating; abandoned town sites such as Port Leon and Magnolia; Leon Sinks Geological Area; the Natural Bridge Battlefield State Historic Site; and the San Marcos de Apalache State Historic Site.

The Wakulla River is a state designated canoe trail used by thousands of people each year for canoeing, manatee watching, and fishing. The St. Marks River also offers an enjoyable paddle, with limited motorboat traffic upstream of the U.S. Highway 98 bridge. The Florida National Scenic Trail crosses the St. Marks River in the town of St. Marks and follows the Tallahassee-St. Marks Historic Railroad State Trail to U.S. Highway 98, crossing the Wakulla River on the highway bridge before reentering the Refuge. The Tallahassee-St. Marks Historic Railroad State Trail follows Florida's oldest rail line (operating from 1837 to 1984 as the Tallahassee-St. Marks Railroad) for sixteen miles to the port town of St. Marks. Since its opening, the trail has been used by approximately 170,000 bicyclists, walkers, skaters, and equestrians each year. Landowners, many of whom were skeptical about the trail before it opened, are now some of its most enthusiastic users.

Growth and Development

Development in the rapidly urbanizing St. Marks River watershed threatens to fragment the river's natural corridor and degrade the water quality of both rivers and the region's groundwater. The upper watershed of the St. Marks River, including Lake Lafayette, receives polluted stormwater runoff from the eastern half of Tallahassee. An industrial park and state prison are planned in northeastern Wakulla County which, because this area is internally drained (via sinkholes) or drains directly into the St. Marks River, may degrade the river and groundwater. Residential development currently lines the west bank of the St. Marks for more than two miles below Natural Bridge and at Newport, fragmenting the river's natural greenway corridor and likely contributing nutrient pollution from septic systems.

The water quality of the lower portion of the St. Marks River has been degraded by petroleum tank farms, petroleum transport barges, a power plant, marinas, wastewater effluent from the city of St. Marks, and urban stormwater runoff. There have been several major and minor oil spills in the past, and river bottom sediments in the area are coated with oil. An effort to dredge polluted sediments from the river was abandoned when a suitable disposal area could not be found.

Wildlife habitat along the Wakulla River has been fragmented by highways and electric transmission lines, and the river's excellent water quality has been degraded by nutrient pollution from septic systems and stormwater runoff from residential and recreational facility development along the river and in adjacent uplands. Heavy recreational use of the river by fast traveling boats poses threats to the West Indian manatee which frequent the river.

Recommendations

The St. Marks and Wakulla Rivers Resource Assessment and Greenway Protection Plan prepared by 1000 Friends of Florida and the Northwest Florida Water Management District, includes recommendations for local, state and federal governments, landowners and recreational users of the St. Marks watershed to help conserve the rivers' outstanding resources. These are highlights of those recommendations:

Recommendations for Local Governments

• Develop a coordinated plan for conserving the St. Marks and Wakulla. Rivers Greenway.
  
• Appoint a St. Marks and Wakulla. Rivers Greenway Advisory Committee to make recommendations to local governments for the adoption of appropriate greenway management and protection measures.
  
• Protect greenways by fee-simple and less-than-fee-simple land acquisition methods and state, federal and private funding to improve recreational facilities.
  
• Form alliances and partnerships between nonprofit organizations, private interests, neighborhood and homeowner associations, local businesses, landowners, and chambers of commerce to promote and manage ecotourism, and to help resolve site development conflicts.

Recommendations for Federal, State and Regional Agencies

• Protect lands within the greenway through acquisition and recreational facility development.
  
• The Northwest Florida Water Management District should prepare a Surface Water Improvement and Management Plan for the St. Marks and Wakulla rivers' watershed.
• The Apalachee Regional Planning Council should establish and provide technical assistance to the proposed St. Marks and Wakulla Rivers Greenway Advisory Committee.
  
  
• The Florida Department of Environmental Protection should develop a public, Land-launch boat access near the St. Marks rise if lands appropriate for such access can be acquired.

Recommendations for Landowners

• Maintain and use native vegetation; limit the amount of vegetation removed near the river.
  
• Access the river using boardwalks instead of paths; limit the use of fertilizers and pesticides.
• Remove or do not construct bulkheads, seawalls and riprap, for bank stabilization.
  
  The St. Marks and Wakulla Rivers are important breeding areas for Mississippi kites, osprey and wood ducks, and are concentration areas for shorebirds, songbirds, wading birds, and waterfowl. Wakulla Springs State Park has preserved habitat for over a dozen rare and endangered ferns and orchids. Rare species that inhabit the river corridors include:
  
  Woodville cave crayfish
  Suwannee bass
  West Indian manatee
  bald eagle
  tricolor heron
  little blue heron
  Wakulla seaside sparrow
  white ibis
  red-cockaded woodpecker
  snowy egret
  limpkin
  warblers (prothonotary, hooded, Kentucky, and Northern Parula)
  wood stork