Canoe Valley comprises approximately 2,000 hectares of lands extending from the coastline east of Farquhars Beach to Port Kaiser (west of Alligator Pond). It spans the parishes of Clarendon and Manchester. The area is comprised of wetlands, beaches and dry limestone forest extending from Farquhar's Beach in Clarendon to Alligator Pond in Manchester. There are both privately and government-owned lands in this area. The area was identified as a potential protected area in the Protected Areas Policy of 1992.

The Alligator Hole River, which falls within the site, was the home of captive manatees. This river was selected for the activity as it was considered the best and safest temporary place for captive manatees. The larger wetland area is also a habitat for the indigenous American crocodile (Crocodylus acutus).

The site comprises a part of the proposed Canoe Valley/Lovers Leap protected area within Jamaica's National Ecological Report (2009) due to its importance for meeting forest habitat goals. Canoe Valley is the only area in which the fish species Gambusia melapleuraoccurs and is the sole contributor to its conservation goal.

The JNHT has conducted extensive archaeological research in the area. There are numerous Taino sites, including settlement, pictograph and petroglyph caves, burial caves, and middens. To date, the area illustrates the highest concentration of Taino sites on the island. The Alligator Hole and marshland would have been an important food source for the Taino (fish, crab, shrimp, manatee and crocodile). The area is under review to be designated Protected National Heritage for both its natural and cultural heritage.