The Alligator Hole River is on the southern border of Manchester and Clarendon. It emerges at the base of Round Hill which is to the east of the river. The river is 1.9km long and empties into Long Bay.

The vegetation in the river is perennial with the embankment protected by Phragmites australis and mangrove roots. The river is part of the wetland system comprising mainly herbaceous vegetation.  

Unless disturbed by man, the water of the river is exceptionally clean.  Proximity to the sea and dissolved salts from the limestone give the river water a salty taste and allow marine and freshwater animals to share the river. The level of the river is affected by tides, rainfall and season blocking of the river mouth by sand. 

This wetland is inhabited by fish, crustaceans (e.g. crabs, shrimp), the American Crocodile, West Indian Manatee, insects (butterflies), birds and plant species.

It is one of five rivers formed at the base of the limestone plateau along the norther edge of Canoe Valley.  The rivers originate from the rainfall on the hills in the centre of the plateau.  Rainwater percolates through the limestone bedrock, forming underground rivers which flow for miles until they emerge at the foot of the plateau.

The water temperature is about 24⁰C (75⁰F) all year round.  Over 460,000cu. M (16 million cu. ft.) of water are estimated to flow out of the mouth of the Alligator Hole River every day.  The river averaged 16m (54ft.) in width and 3m (10ft.) in depth.  It flows at 0.4kmph (0.025 mph).