We present here a copper speciation model that accounts for the long-term ('coastal-acidification') and short-term (daily and seasonal variation) variability in water pH and water temperature. The developed model is applied to a sub-tropical estuary (Moreton Bay, Australia) at a one hundred year time scale so that outputs are consistent with climate change projections. The model predicts that the mean cupric ion concentration (Cu2+) in the estuary will increase by 115% over the next 100 years as a result of the projected decrease in pH and increase in water temperature. Through calibration, the estimated concentration of copper-complexing dissolved organic matter (DOM) in the estuary is found to be 22.5 nM. An increase in the concentration of Cu2+, which is the most toxic and bioavailable form of copper, has implications for ecosystem health and may have a negative effect on the detoxifying capacity of DOM. Models that provide a framework for coupling biological, chemical and physical processes are important for providing a holistic perspective of coastal systems, especially for better understanding a system within the context of climatic and non-climatic drivers.