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Natural and human disturbance along with climate change pose major challenges for resource management. This is relevant in natural forests, where conflict can occur between water provision and industrial logging. As a result, conversion of old forests to young, fast-growing stands through logging can dramatically reduce streamflow and water yield. We modelled changes in stream run-off and hence water yield from a forest catchment in response to clearcut logging and compared this with projected climate change (using a Representative Climate Futures [RCFs] approach). We focused on the Thomson Catchment, which is the largest single catchment for the city of Melbourne, south-eastern Australia. Within this catchment, we targeted our analysis at montane ash-type eucalypt forests, as these receive the most rainfall and are subject to clearcutting. We used several forest management scenarios to model changes in water yield over time. For our analysis of projected climate change, we employed a range of RCFs that represent ‘consensus’, ‘wettest’ and ‘driest’ scenarios to model the impacts of multiple Representative Concentration Pathways (RCPs). Our initial spatial analysis revealed that 42% of the ash-type eucalypt forests in the Thomson Catchment have been logged. Under historical and continued logging, stream runoff decreases by 40,211 ML by 2090 compared with a hypothetical baseline if logging had ceased in 1995 and 34,059 ML if logging continues beyond 2019. These losses exceed the projected impacts of climate change under the consensus and wettest scenarios, but the driest scenarios are projected to exceed these losses, consisting of 49,998 ML and 69,474 ML for RCP 4.5 and RCP 8.5, respectively. We suggest logging be excluded from the Thomson Catchment because of decreasing stream flows due to climate change and an increasing water demand due to human population growth. This study provides a quantitative approach for highlighting how resource conflicts can be magnified under climate change.