Environmental water represents a key resource in managing freshwater ecosystems against pervasive threats. The impacts of climate change add further pressures to environmental water management, yet anticipating these impacts through modelling approaches remains challenging due to the complexities of the climate, hydrological and ecological systems. In this paper, we review the challenges posed by each of these three areas. Large uncertainties in predicting climatic changes and non-stationarities in hydrological and ecological responses make anticipating impacts difficult. In addition, a legacy of relying on modelling approaches informed by historic dependencies in environmental water science may confound the prediction of ecological responses when extrapolating under novel conditions. We also discuss applying ecohydrological methods to support decision-making and review applications of bottom-up climate impact assessments (specifically eco-engineering decision scaling) to freshwater ecosystems. These approaches offer a promising way of incorporating climatic uncertainty and balancing competing environmental objectives, but some practical challenges remain in their adoption for modelling environmental water outcomes under climate change.