The Montseny brook newt (Calotriton arnoldi) is a critically endangered amphibian species which inhabits a small 20 km2 holm oak and beech forest area in NE Spain. Calotriton arnoldi strictly lives in running waters and might be highly vulnerable to hydrological perturbations expected to occur under climate and vegetation cover changes. Knowledge about the potential response of the species habitat to environmental changes can help assessing the actions needed for its conservation. Based on knowledge of the species and supported by observations, we proposed daily low and high streamflow event thresholds for the viability of C. arnoldi. We used the rainfall–runoff model PERSiST to simulate changes in the frequency and duration of these events, which were predicted under two climate and four vegetation cover scenarios for near‐future (2031–2050) and far‐future (2081–2100) periods in a reference catchment. All future scenarios projected a significant decrease in annual streamflow (from 21% to as much as 67%) with respect to the reference period. The frequency and length of low streamflow events will dramatically increase. In contrast, the risk of catastrophic drift linked to high streamflow events was predicted to decrease. The potential change in vegetation toward an expansion of holm oak forests will be more important than climate changes in determining threshold low flow conditions. We thus demonstrated that consideration of potential changes in vegetation and not only changes in climate variables is essential in simulating future streamflows. This study shows that future low streamflow conditions will pose a severe threat for the survival of C. arnoldi and may help taking management actions, including limiting the expansion of holm oak forest, for ameliorating the species habitat and help its conservation.