Biscayne Bay is a shallow estuary. It is a place where freshwater from the mainland mixes with salt water from the sea. The bay serves as a nursery for marine life. Lush seagrass beds provide hiding places as well as food for a vast array of sea life.

Biscayne Bay is primarily a saltwater (saline) tropical lagoon, but it is technically classified as an estuary because it receives freshwater inflow from the Florida mainland. The bay's salinity levels fluctuate based on proximity to the Atlantic Ocean and the amount of freshwater discharged through canals and rivers like the Miami River. Historically, the bay featured many freshwater springs, but modern drainage and development have shifted the balance, making the water more consistently salty. The mixing of these waters creates a brackish environment in certain areas, which is vital for the health of local seagrasses and mangrove forests. These habitats support a diverse range of marine life, including manatees, sea turtles, and hundreds of species of fish. Maintaining the delicate balance of saltwater and freshwater is a major focus of environmental restoration efforts in the Miami area today.