Extinction risk of natural populations of animals and plants is enhanced by many different processes, including habitat size reduction and toxic chemical exposure. We develop a method to evaluate different risk factors in terms of the decrease in the mean extinction time. We choose a population model with logistic growth, environmental and demographic stochasticities with three parameters (intrinsic growth rate r, carrying capacity K, and environmental noise sigma(2)(e)). The reduction in the habitat size decreases carrying capacity K only, whilst toxic chemical exposure decreases survivorship (or fertility) and in effect reduces both r and K. We derived a formula for the reduction in habitat size that decrease the mean extinction time by the same magnitude as a given level of toxic chemical exposure. In a large population (large K) or in a slowly growing population (small r), a small decrease in survivorship can cause the extinction risk increase corresponding to a significant reduction in the habitat size. This conclusion depends also on the nonlinearity of dose-effect relationship. To illustrate the method, we analyse a freshwater fish, Japanese crucian carp (Carassius auratus subsp.) in Lake Biwa.