Freshwater resources need to simultaneously support environmental and agricultural outcomes; this is a critical challenge under climate change. Many environmental and agricultural outcomes have contrasting requirements for water, leading to difficult trade-offs which should be supported by integrated assessments. Here we analysed the effect of climate change and climate variability on key ecological values and agricultural economic activity simultaneously in the Macquarie catchment in Australia and assessed the effect of plausible management adaptation options. Under severe climate change, ecological outcomes were rarely met while the impact on agricultural outcomes was less severe; annual cropping reliant on insecure water allocations was most vulnerable. Under moderate climate change, altering flow delivery patterns was as effective as altering the total licence volume of environmental water. Neither change adversely affected agricultural benefits. Thus, environmental water management can potentially influence environmental outcomes, while continuing to meet the needs of core agricultural activities.