Despite being an estuary, the waterway is called a lagoon because the River is a body of water separated from the ocean by a barrier island, with limited exchange with the ocean through the inlets. The Lagoon varies in width from one-half mile to five miles and averages about three feet in depth, serving as a spawning and nursery ground for both ocean and lagoon fish. It has one of the most diverse bird populations anywhere in America. Nearly one-third of the nation's manatee population lives here or migrates through the Lagoon.

The Indian River Lagoon is North America's most diverse estuary with more than 4,000 animal and plant species, including manatees, dolphins, sea turtles, seahorses and all seven varieties of the sea grasses found in the state of Florida. The River's more than 2,200 species of animals include 700 types of fish, 68 reptiles and amphibians, 370 birds and 29 animals; the most in any North American estuary. In addition, there are 2,100 types of plants. Located in the zone where tropical and temperate climates meet, its flora and fauna as a result include some tropical and subtropical species that cannot survive cold weather along with other species that can. Much of the area is a critical habitat for the many species of animals classified as threatened or endangered.

The Atlantic Flyway, the route used by the millions of birds thatmigrate between eastern North America and South America and the Caribbean, is located over the Estuary. Some of the birds get as far as the Lagoon and decide to forego the rest of the trip south, residing here as happily as those of us who have chosen this as our home.

The islands in the middle of the Lagoon are man-made spoil islands, created in the 1950's from the dredging of the Intra-coastal waterway to allow shipping to come inland. The lagoon extends from the Ponce de Leon Inlet in Volusia County to the Jupiter Inlet in Palm Beach County. The channel averages 12 feet in depth. When the channel was created, sludge and muck were dug out and dumped in the water, and much of the sea grass was destroyed. However, over the years, the islands that formed have stabilized, and sea grasses have colonized portions of the submerged areas. Mangroves, the glue of Florida, have helped form the many islands which now exist, providing nesting sites for terns and other shore birds whose natural nests are on beaches which have often been disturbed by humans.