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Apalachicola Bay is home to one of the largest and most renowned commercial oyster fisheries in the world, and it is an important area for brown shrimp, scallops and blue crabs as well. Anglers flock to the region to fish for spotted seatrout, redfish, tarpon, Spanish mackerel, sheepshead, dolphin, cobia, flounder, and several grouper and snapper species. In 2005, retail sales associated with saltwater recreational fishing in Gulf and Franklin counties totaled $108 million, supporting nearly 2,000 jobs.

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Much of the Apalachicola coastal region has been set aside as protected, which has helped maintain the area's fish and wildlife populations. However, an unresolved water dispute with Georgia over minimum flows and levels, substantial water diversions and polluted runoff associated with urban development and agricultural activities inland have caused significant water quality problems in Apalachicola Bay and surrounding waters, and those problems are expected to become worse as the region's human population continues to grow. With the added stressors associated with sea-level rise, reductions in water quality and changes in habitat due to these multiple threats could have serious consequences for the area's fisheries.

Sea-level rise is projected to cause a 61-percent decline in important saltmarsh habitat in Apalachicola Bay by 2100, making coastal waters and seagrass beds more vulnerable to polluted runoff. Inundation also is expected to cause a significant decline in hardwood swamp area, particularly along the Apalachicola River, where swamp elevations are low relative to sea level.

An estimated 13 to 16 percent of these swamps are expected to convert to brackish marsh, which had been virtually non-existent at this site. Some tidal and inland freshwater marsh is projected to become inundated and converted to brackish marsh as well. In addition, inundation and saturation are projected to convert more than a quarter of the dry land on this site, primarily along the river basin; and overwash is expected to have a significant effect on the barrier islands to the south of this site.

Species that would face the greatest impact from saltmarsh and seagrass loss in Apalachicola include the oyster, flounder, spotted seatrout, redfish, tarpon and young gag grouper. The region's brown shrimp and blue crabs also are vulnerable to declines in essential habitat, which could reduce available food sources for many of the region's gamefish species.