Climate change and land-use change are having substantial impacts on biodiversity worldwide, but few studies have considered the impact of these factors together. If the combined effects of climate and land-use change are greater than the effects of each threat individually, current conservation management strategies may be inefficient and/or ineffective. This is particularly important with respect to freshwater ecosystems because freshwater biodiversity has declined faster than either terrestrial or marine biodiversity over the last three decades. This is the first study to model the independent and combined effects of climate change and land-use change on freshwater macroinvertebrates and fish. Using a case study in southeast Queensland, Australia, we built a Bayesian Belief Network populated with a combination of field data, simulations, existing models, and expert judgment. Different land-use and climate scenarios were used to make predictions on how the richness of freshwater macroinvertebrates and fish is likely to respond in the future. We discovered little change in richness averaged across the region but identified important impacts and effects at finer scales. High nutrients and high runoff as a result of urbanization combined with high nutrients and high water temperature as a result of climate change, and were the leading drivers of potential declines in macroinvertebrates and fish at fine scales.Synthesis and applications. This is the first study to separate out the constituent drivers of impacts on biodiversity that result from climate change and land-use change. Mitigation requires management actions that reduce in-stream nutrients, slows terrestrial runoff, and provides shade, to improve the resilience of biodiversity in streams. Encouragingly, the restoration of riparian habitats is identified as an important buffering tool that can mitigate the negative effects of climate change and land-use change. This article is protected by copyright. All rights reserved.