Everglades (ENP) and Biscayne National Parks (BNP) contain coastal marine environments characterized by coral reefs, mangrove islands, seagrass beds, and a variety of other tropical marine benthic habitats. The close proximity of BNP to a major metropolitan area and agricultural region has raised concern for the health of this marine resource. A critical geological attribute of healthy coral reef environments is the ability of reefs to produce calcium carbonate. Monitoring rates of key metabolic processes such as calcification, photosynthesis, and respiration (collectively termed productivity) provides a method for quantifying reef health in terms of system functionality. This enables geographic comparisons of system health between different reef environments. Productivity rates associated with representative benthic habitats in BNP were measured using a Submersible Habitat for Analyzing Reef Quality (SHARQ), a large incubation chamber, to enclose 8.7 m3 of seawater above 11 m2 of seafloor and measure geochemical changes resulting from benthic metabolism. The large surface area and water volume isolated by the SHARQ enables 24-hour, community-level productivity measurements for several substrate types including live rock, coral and coral rubble, live sand, and seagrass communities. Continued, seasonal monitoring of productivity in BNP and comparison to other reef environments will aid in assessing the health of this environment. In ENP, monitoring has focussed on grass beds in Florida Bay. Additionally, the SHARQ provides a mechanism for in situ alteration of environmental parameters (such as turbidity, salinity, nutrients, dissolved oxygen, and carbon dioxide), and can be used for experimentation in addition to monitoring. The SHARQ (patent pending) enables investigations on the response of coastal benthic communities to environmental stress resulting from natural and anthropogenic influences.