•A critical ecological threshold was determined between simulation years 25 and 50.•Unacceptable risk was reached before the threshold under laissez-faire strategy.•Crossing the threshold increased greatly the risk of reducing the whale abundance.•At simulation year 25 there was an average of 60 whale watching boats.•Establishing a legal maximum below 60 whale watching boats reduced the risk. Policy-making to protect threatened species implies dealing with uncertainty and ignorance. Conservation management of the Eastern gray whale (Eschrichtius robustus) population through the regulation of whale watching in the lagoon Ojo de Liebre, Mexico, is a useful example of policy-making challenged by lack of scientific knowledge regarding the negative long-term effects of whale watching. We present a pragmatic approach to provide Mexican authorities the technical information they need to justify the establishment of a maximum number of boats under conditions of deep uncertainty. Operationally, our approach combines system dynamics modelling, to simulate the boats’ impact on the breeding habitat, with ecological risk assessment, to determine the probability of crossing a critical ecological threshold, which is associated to a risk of severely reducing the gray whale abundance in the lagoon. Thus, our approach addresses the issue of establishing a legal maximum number of boats to protect threatened species.