Habitat loss and fragmentation from agricultural expansion and infrastructure development are primary threats to the survival of the Chinese alligator, as wetlands have been extensively drained and isolated. The remaining habitat is further degraded by water pollution, including fertilizer and pesticide runoff, which diminishes water quality and the alligator’s prey base. Alligators were poisoned through poisoning campaigns targeting rats and snails, both prey items of the species. Direct persecution, natural disasters (floods and drought), geographic separation, and low reproductive productivity also contributed to the species' decline.
Although the Chinese alligator is now legally protected, enforcement of conservation regulations has been largely ineffective. Human-related pressures—from the legacy of past over-hunting to ongoing habitat encroachment—continue to undermine the species’ recovery. Together, these ecological and anthropogenic threats jeopardize the Chinese alligator and its freshwater wetland ecosystem, leaving the species perilously close to extinction.