Widely regarded as a keystone species and ecosystem engineer, the eastern oyster Crassostrea virginica plays a vital role in estuarine environments. Complex, three-dimensional oyster reefs act as havens for biodiversity and contribute to ecological processes. Recently, concern for this resource has arisen in Mosquito Lagoon, Florida, the southernmost limit along the Atlantic coast for undisturbed, intertidal reefs of C. virginica. Since the 1990s, intense recreational boating activity has caused atypical dead margins (mounds of disarticulated shells) to emerge on the seaward edges of oyster reefs located along major navigational channels. Once dead margins are formed, little is known about their influence on biotic composition and interactions on oyster reefs. This study focused on the affect of dead margins on: (1) mobile species biodiversity and distribution, (2) reef architecture, and (3) the affect of structural variables on predation of juvenile oysters. To determine if dead margins influenced the biodiversity of mobile species on oyster reefs, lift nets (1 m2) were deployed within Mosquito Lagoon for one year (June 2004 - June 2005). These nets (5/site) were deployed on the back-reef areas of six reefs (3 reference reefs and 3 reefs containing dead margins). To simulate reef habitat, one and a half liters of live oysters were placed within each net. Lift nets were checked monthly and surveyed for all mobile species. The resulting data were assimilated into a species inventory containing 65 species of fishes, mollusks, crustaceans, worms, and echinoderms. The two most abundant species present on reefs in Mosquito Lagoon were the big-claw snapping shrimp Alpheus heterochaelis, a filter-feeder, and the flat-back mud crab Eurypanopeus herbstii, a predator of oyster spat. Contrary to expections, analyses of community metrics showed that dead margins did not significantly affect the biodiversity of back-reef areas on oyster reefs. Modified lift nets (0.25 m2) were placed on six different oyster reefs (3 reference reefs and 3 containing dead margins) to test if dead margins affected the distribution of mobile species inhabiting oyster reefs. Nine nets were arranged to cover three separate areas of each reef: the fore-reef (3 nets), mid-reef (3 nets), and back-reef (3 nets). Half a liter of oyster shells were placed inside each net. These nets were checked weekly, for five weeks and species richness, density, and biomass were recorded. Analyses revealed that all community metrics were significantly higher on reference reefs than reefs affected with dead margins. Further, a significant drop in all three metrics was seen on the mid-reef area of affected reefs. The absence of species on this area is hypothesized to be due to a lack of water, shade, and habitat complexity. To document architectural differences, two types of transects were run along five reference reefs and five reefs with dead margins. First, quadrat transects determined the percent of live oysters, the percent of shell clusters, topographic complexity (using chain links), and the angle of shells on each reef type. Transect lines were stretched parallel to the water line and covered all three reef areas (fore-reef, mid-reef, and back-reef). The results showed reference reefs to have approximately four-fold more live oysters, approximately twice as many shell clusters, and significantly greater topographic complexity. Numbers of live oysters and shell clusters were greater on the fore-reef and back-reef areas of both reef types. Second, laser transects were used to record reef profiles and the slope of fore-reef areas. Transect lines were stretched perpendicular to the water line and every 20 cm the distance between the lagoon bottom and reef top was measured. Vertical reef profiles and fore-reef slopes were significantly different between reference reefs and reefs with dead margins. Dead margins compressed reef widths, increased center peaks, and increased slopes on the fore-reef area by two-fold. Lastly, field experiments were conducted to determine the affect of dead margins on the vulnerability of oyster spat to predation. Structural variables (e.g. shell orientation, single versus shell clusters, reef slope) were manipulated and effects on oyster mortality were observed. Three predators were tested: the blue crab Callinectes sapidus, the common mud crab Panopeus herbstii, and the Atlantic oyster drill Urosalpinx cinerea. Structural variables did not have a significant influence on oyster mortality; however, a significant difference was established between predators. Panopeus herbstii consumed the most juvenile oysters, followed by U. cinerea and then C. sapidus. Together, these findings document ecological implications of dead margins on C. virginica reefs and reinforce the urgent need for enhanced regulations and restoration. If the intensity of recreational boating remains unregulated, dead margins will continue to increase. Thus, in order to maintain the diversity and productivity of Mosquito Lagoon, it is crucial to fully understand how dead margins alter the biogenic habitat and biotic communities of oyster reefs.