Freshwater ecology is a profoundly important applied discipline in Australia and has focussed effectively on engaging with the needs of policy makers and managers. However freshwater systems are also fantastic models for addressing and generating fundamental ecological theory. Reviewing existing and emerging areas of ecological theory, I will identify some key areas where freshwater ecology can contribute. Using five case studies of research from Australia, I will illustrate how powerful freshwater systems can be for testing theory. There is an important question mark over whether the latest investments in freshwater monitoring are being leveraged as much as they could be to answer the big questions that still drive ecology in other ecosystems.