The Adelaide River is well known for its high concentration of saltwater crocodiles, along with other wildlife including white-bellied sea eagles, whistling kites, freshwater crocodiles, bull sharks and Black Flying-fox. Waters of this river are also home to endangered speartooth shark and critically endangered large tooth sawfish.

The floodplains have been identified as an Important Bird Area they support over 1% of the world populations of several species of waterbirds, including magpie geese (up to 800,000), wandering whistling ducks (188,000) pied herons (2000), red-necked avocets, (3000), little curlews, (12,000), far eastern curlews (1050), and sharp-tailed sandpipers (2500). There are large breeding colonies containing 30,000 mixed waterbirds, significant numbers of bush stone curlews and 11 other species that have restricted ranges.

The river is tidally influenced along a large portion of its length, with tidal movements in the Spectacular Jumping Crocodile area, regularly being in the 6.5-7.5 metre mark.

In this area, the river is approximately 5-6 metres in depth. This large volume of water movement is why the river looks so dirty, the fine sediments rarely get a chance to settle and constantly on the move, however despite its look, the river is very clean and free for the most part of any pollutants from industry or agriculture. During a typical wet season, due to the large collection or feeder area, the river will break its banks and spread those fine nutrient sediments across the floodplain. During the recent 2018 record floods, the river was approximately 120cm deep through the Spectacular Jumping Crocodile carpark and the river was approximately 20km wide at places.