Large wood governs channel morphology, as well as the availability of in‐stream habitat, in many forested streams. In this paper, we use a stochastic, physically based model to simulate wood recruitment and in‐stream geomorphic processes, in order to explore the influence of disturbance history on the availability of aquatic habitat. Specifically, we consider the effects of fire on a range of stream sizes by varying the rate of tree toppling over time in a simulated forest characterized by a tree height of 30 m. We also consider the effects of forest harvesting with various riparian buffer sizes, by limiting the lateral extent of the riparian stand. Our results show that pulsed inputs of wood increase the availability and variability of physical habitat in the postfire period; reach‐averaged pool area and deposit area double in small streams, while side channels increase by over 50% in intermediate‐sized channels. By contrast, forest harvesting reduces the availability of habitat within the reach, though the effects diminish with increasing buffer size or stream width; in laterally stable streams the effects are minimal so long as buffer width is large enough for key pieces to be recruited to the reach. This research emphasizes the importance of natural disturbance in creating and maintaining habitat heterogeneity and shows that scenario‐based numerical modeling provides a useful tool for assessing the historical range of variability associated with natural disturbance, as well as changes in habitat relevant to fish. It can be also used to inform forest harvesting and management.