The waters of the Indian River Lagoon in Brevard County are considered to be critical habitat for the endangered Florida manatee (Trichechus manatus latirostris). The presence of a warm water refuge, seagrass beds for forage, and protected areas in the north Banana River also make Brevard County attractive habitat for manatees. Brevard County has been described as the "hub" of the east coast manatee population and large numbers of manatees can be found in Brevard County waters year-round. Manatees using Brevard County can be divided into three major groups: manatees that spend the cooler months in south Florida and migrate to Brevard during warmer months, manatees that spend the cooler months in Brevard and migrate further north along the Florida coast during the warmer months, and manatees that spend all year in Brevard and the surrounding counties. During the spring and fall, manatees from all three groups can be found in Brevard. The largest spring and winter manatee aggregations (groups of manatees in the same area) in the state of Florida have been recorded in Brevard County. Spring aggregations in the north Banana River alone have exceeded 365 manatees, while winter surveys at Brevard’s warm water refuges have documented at least 529 manatees.

Brevard County also has the highest number of manatee mortalities (deaths), including the highest number of watercraft-related manatee mortalities, of any county in the State. From June of 1974 through 1995, there were 2613 manatee mortalities documented in Florida. Approximately 20% (523) of the manatee mortalities recovered in Florida were from Brevard County waters. Human-related causes of death include watercraft collisions, deaths due to water control structures, accidental feeding on trash, and entanglement in fishing line. Of the manatee mortalities recovered from Brevard County from June 1974 - 1995, 28% (147) were "undetermined", 26% (138) were attributed to perinatal mortality (young manatees less than 130 cm), 24% (125) were attributed to watercraft, 19% (98) were attributed to other natural causes, 2% (9) were attributed to other human causes, and 1% were attributed to flood gate/canal locks. For most of the manatee deaths recorded as "undetermined", the manatee’s body was too badly decomposed to determine a cause of death.

A major threat to the long term survival and recovery of the manatee population is the loss of habitat. Brevard County has experienced rapid population growth since the development of Kennedy Space Center in the mid-1960’s. Most of this growth concentrated along the shores of the Indian River Lagoon and the beaches. Extensive development with poor soil conservation practices, storm water runoff, the loss of wetlands that border the lagoon, and the discharge of large amounts of treated sewage into the lagoon has, over time, degraded the water quality of the Indian River Lagoon. As the Indian River Lagoon’s water quality became degraded, the seagrass beds declined. Recent studies on seagrasses in the Indian River Lagoon indicated that a 6% loss of seagrass from the lagoon occurred between the 1940’s and 1990’s. This loss over a fifty year period, however, can be misleading. While there are areas of the lagoon that have shown a stable or increasing seagrass community, there are other large areas that have shown dramatic declines. The areas that have experienced the most loss of seagrass are primarily located near the urban areas. In some instances, nearly 90 to 100% of the original seagrass areas have disappeared. Today, there are many programs working toward the goal of improving the Indian River Lagoon; and there are rules and regulations in place that try to prevent the kinds of damage to the lagoon that happened in the past from happening again.

High numbers of human-related deaths and human activity related impacts to manatee habitat, combined with the manatee’s slow reproductive rate, contributes to the Florida manatee being at risk of extinction. A more detailed description of the manatee’s life history, biology, abundance, mortality, and habitat is contained in the text of the Brevard County Manatee Protection Plan.