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Refuge staff monitors the beach-nesting bird populations monthly by recording numbers of nesting pairs, spring and fall migrants, and wintering birds. Refuge staff follows Florida Fish and Wildlife Conservation Commission's (FWC) Breeding Bird Protocol (numbers and locations of nesting pairs) and FWC's Monitoring Protocol for Non-Breeding Shorebirds and Seabirds (numbers and locations). Data is entered into the Florida Shorebird Database. Approximately 40,000 pairs of beach-nesting birds are recorded annually.

Sea turtle nesting is documented according to FWC's protocol for monitoring Florida Index Nesting Beaches. Thirty to 70 loggerhead sea turtles nest annually on Egmont Key. 

Additional research is conducted by university students under special use permits and includes: monitoring the gopher tortoises (population, sex ratio, habitat preference), box turtles (population, sex ratio, habitat preference, food preference) and beach erosion (rate). About 1200 gopher tortoises and 700 box turtles live on Egmont Key. The beach is rapidly eroding from hurricanes and tropical storms and sea level rise.