Coastal marine construction and dredging operations typically require specific permit conditions in order to reduce the risk of injury or death to a variety of endangered and protected species including manatees, sea turtles, and bottlenose dolphins. In Florida, these activities are managed by the Florida Department of Environmental Protection (FDEP) and the three water management districts (St. Johns River, Southwest Florida, and South Florida). Dredging activities are also regulated by the federal government under a separate program administered by the U.S. Army Corps of Engineers. If projects involve potential impacts on protected and endangered species, additional input is typically provided by both the Florida Fish and Wildlife Conservation Commission and the U.S. Fish and Wildlife Service.

The Sea2Shore Protected Species Monitoring Program provides certified experienced observers in order to help organizations involved with dredging and construction operations to comply with state and federal permit guidelines. The types of monitoring may include land-based monitoring, boat-based monitoring, or aerial surveillance. The types of projects which Sea2Shore staff has assisted with include bridge demolitions, waterside blasting, and several bucket, clamshell, and cutter section dredging operations.

Sea2Shore staff also has been involved with endangered and protected species surveillance in association with high-speed marine events including the Suncoast Offshore Grand Prix in Sarasota and the Hurricane Offshore Classic in St. Petersburg. Additional protected species monitoring has also been performed during the Gasparilla Boat Parade in Tampa Bay. During the summer of 2009, Sea2Shore provided several experienced observers to monitor a 24-hour, two-month-long channel dredging operation conducted in Tampa Bay by Great Lakes Dredge and Dock Company.