Wildlife-based tourism poses opportunities and challenges for species conservation. Minimizing potential negative impacts of tourism is critical to ensure business and conservation enterprises can coexist. In north-western Namibia tourism is used as a conservation tool for the Critically Endangered black rhinoceros Diceros bicornis. However, black rhinoceroses are susceptible to human disturbance and may become displaced by tourist activities, which threatens not only the security and health of the rhinoceros population but also the sustainability of the business. We examined areas avoided by black rhinoceroses to understand how they respond to the type and extent of tourism development, and to evaluate management alternatives. We used spatial data on use of water sources by rhinoceroses to create a series of a priori candidate models that described the negative influences of tourist activities on rhinoceros habitat use. A model selection approach strongly supported a cumulative zones of influence model comprised of a 6 km buffer around the airstrip combined with a 1 km buffer around roads used daily. We compared alternative management scenarios using the best-performing model and found that an optimal road-use policy combined with airstrip relocation could minimize the total area avoided by the black rhinoceros to 7.1% and loss of high quality habitat to 20.7%. Under the worst-case scenario the area avoided and loss of high quality habitat were 153 and 85% greater, respectively, than under the scenario with optimal management. Our findings provide a novel framework and a practical, policy-relevant decision support tool to improve the contribution of tourism to wildlife conservation.