Feral (wild) horses present significant challenges for landscape managers. A major effect of horses is trampling, which erodes soil and alters vegetation cover, which is often critical habitat for threatened animals. We examined the direct and indirect impacts of horses, kangaroos, and rabbits on the broad-toothed rat (Mastacomys fuscus), a threatened rodent in subalpine grasslands in Kosciusko National Park, which contains a large wild horse population. Our objective was to examine the relationship between the activity of different herbivores and 1) structural attributes of the vegetation (cover and density of different plant groups) and 2) length of broad-toothed rat runways and the presence of scat along these runways as proxies of broad-toothed rat activity. We assessed herbivore activity and measured vegetation cover, structure, and richness and total length of runways used by broad-toothed rats as a measure of activity. We used structural equation modeling to test the hypothesis that horse activity would lead to reductions in rat habitat directly, by increasing disturbance, and indirectly, by altering vegetation structure. Quadrats showing no evidence of horse activity had longer broad-toothed rat runways, taller but fewer grasses, double the shrub cover, and lower plant richness than quadrats showing evidence of horse activity. Structural equation modeling showed that there were no significant direct associations between horse activity and rat activity. However, increasing horse activity was associated with an indirect negative effect on broad-toothed rat activity by suppressing the positive relationship between grass height and rat activity. There were no significant effects of rabbits on any environmental variables, and kangaroo grazing was associated with an increase in shrub cover only. Disturbance by horses likely alters vegetation structure, by reducing grass height, making it less suitable for broad-toothed rats, thereby reducing their populations. Horses should be restricted from accessing critical broad-toothed rat habitat.