Manatees also use the Port area for playing, resting, reproduction, feeding, freshwater drinking, and as a warm-water refuge. Manatees have been observed entering the Port through the lock in the morning and then returning to the Banana River through the lock at sundown. The lock tenders frequently have reported observing manatee-mating behavior at both the eastern and western entrances of the lock. The Canaveral Lock therefore is one of the few places where estrus behavior has been and can be observed and monitored. Canaveral Lock is also one of the U.S. Army Corps of Engineers' most active navigational structures.
Daily traffic includes numerous recreational vessels, commercial fishing boats, and fuel barges.
With the combination of the high frequency use of this area by both manatees and people, there is a correspondingly high structure-related mortality rate. According to the Department of Environmental Protection Bureau of Protected Species, there were four mortalities attributed to the Canaveral Lock in 1996, and more than ten since these records have been kept. In response to the concerns over the deaths, manatee detection devices have been designed. The most promising of the new detection technologies for navigation structures is the Acoustic Ladder Array. Under contract with the U.S. Army Corps of Engineers, Harbor Branch Oceanographic Institute designed the system, which is used at Canaveral Lock.