Northern Australia is a land of climate extremes and aquatic biota have adapted to these conditions. Under global warming, extreme El Niño-Southern Oscillation events are predicted to increase but may become more difficult to predict. Using two case-studies, we show that novel modelling approaches can be used to test robustness of management approaches to extreme environmental variability. Short-lived, fast-growing species, such as prawns and mud crabs, are highly sensitive to fluctuations in the environment. For redleg banana prawns, we assessed the performance of harvest control rules based on static, dynamic or a mix of static and dynamic reference levels under three potential climate futures: dry (more El Niños), intermediate and wet (more La Niñas). We found the greatest difference in the performance of HCRs under a future dry climate, but little difference under a future wet climate. For mud crabs, we assessed the impacts of water extraction from rivers with and without accounting for future climate scenarios and found that impacts to biomass and catch weren’t always as expected, highlighting the importance in accounting for nonlinear interactions and trophic links. Improving climate preparedness in management practices will be vital to help safeguard fish stocks and industries in the future.