Its deep water habitat includes salt domes, which are underwater mountains, and the reef-building corals that live on top of those formations. Those who visit for sportfishing and diving can see coral heads bigger than cars and a bounty of wildlife including whales, sea turtles, mollusks, crustaceans, birds, rays, and hundreds of species of fish. Below the coral cap in deeper water are additional species including gorgonians and black corals.

While Flower Garden Banks offers outstanding recreation, its distant location makes it a major center for research and conservation activities, many of which are supported by the National Marine Sanctuary Foundation.

Since 2011, the Foundation funded annual scientific cruises to monitor the health of the coral in the sanctuary. Researchers record conditions and detect early warning signs including impact of climate change and potential environmental crime. Scientists use the long-term data to establish baselines, understand changes and assess why reefs become unhealthy. This ongoing record was invaluable in 2016 when the Sanctuary discovered a massive coral die-off in its East Bank. While the event has stabilized, the Foundation continues to commit additional funding to support further monitoring. The Foundation also funds economic impact studies on commercial and recreational activity in the area to understand use and inform protection planning and potential expansion.