Climate change is impacting ecosystems worldwide. Estuaries are diverse and important aquatic ecosystems; and yet until now we have lacked information on the response of estuaries to climate change. Here we present data from a twelve-year monitoring program, involving 6200 observations of 166 estuaries along >1100 kilometres of the Australian coastline encompassing all estuary morphologies. Estuary temperatures increased by 2.16 °C on average over 12 years, at a rate of 0.2 °C year⁻¹, with waters acidifying at a rate of 0.09 pH units and freshening at 0.086 PSU year⁻¹. The response of estuaries to climate change is dependent on their morphology. Lagoons and rivers are warming and acidifying at the fastest rate because of shallow average depths and limited oceanic exchange. The changes measured are an order of magnitude faster than predicted by global ocean and atmospheric models, indicating that existing global models may not be useful to predict change in estuaries.

So as to assess how emerging science and new tools can be applied to study multiple stressors at a large (ecosystem) scale and to facilitate greater integration of approaches among different scientific disciplines, a workshop was organised on 10–12 September 2014 at the Sydney Institute of Marine Sciences, Sydney, Australia. The present paper discusses the limitations of the current risk-assessment approaches and how multiple stressors at large scales can be better evaluated in ecological risk assessments to inform the development of more efficient and preventive management policies based on adaptive management in the future. A future risk-assessment paradigm that overcomes these limitations is presented. This paradigm includes cultural and ecological protection goals, the development of ecological scenarios, the establishment of the relevant interactions among species, potential sources of stressors, their interactions and the development of cause–effect models. It is envisaged that this will be achievable through a greater integration of approaches among different scientific disciplines and through the application of new and emerging tools such as 'big data', ecological modelling and the incorporation of ecosystem service endpoints.