1. Freshwater cetacean species, including the baiji (Lipotes vexillifer), Amazon River dolphin (Inia geoffrensis), Ganges/Indus River dolphins (Platanista spp.) and Yangtze finless porpoise (Neophocaena asiaeorientalis asiaeorientalis), apex predators in megariver ecosystems, face serious challenges owing to the deterioration of habitat quality.
2. We simulated population change of four freshwater cetacean species under increasing habitat deterioration. Carrying capacity (K) was used to represent the habitat quality, and a logistic model was used to describe the rate of habitat deterioration (dK).
3. An individual-based Leslie matrix model showed that population declines and extinctions in freshwater cetaceans under increasing habitat deterioration exhibit a consistent pattern irrespective of the initial level of K or population size. When dK is low, population abundance fluctuates stochastically around initial K, but a rapid increase in dK is accompanied by a sharp population decline, with a residual population ultimately declining continuously to extinction.
4. Simulations show that traditional census survey techniques used in cetacean species are unlikely to detect early signs of population decline before a critical level is reached.
5. Empirical data of the likely extinction of baiji strongly agree with our simulation exercise, implying that extinction of other freshwater cetacean species may occur sooner than previously considered. Hence, precautionary approaches for habitat restoration and landscape management should be implemented before freshwater cetacean population declines are detected, and ideally, before habitat quality begins to deteriorate.