1. Changes in land management (land use and land cover) and water management (including extraction of ground water and diversion of surface waters for irrigation) driven by increases in agricultural production and urban expansion (and fundamentally by population growth) have created multiple stressors on global freshwater ecosystems that we can no longer ignore. 2. The development and testing of conceptual ecological models that examine the impact of stressors on aquatic ecosystems, and recognise that responses may be nonlinear, is now essential for identifying critical processes and predicting changes, particularly the possibility of catastrophic regime shifts or ‘ecological surprises’. 3. Models depicting gradual ecological change and three types of regime shift (simple thresholds, hysteresis and irreversible changes) were examined in the context of shallow inland aquatic ecosystems (wetlands, shallow lakes and temporary river pools) in southwestern Australia subject to multiple anthropogenic impacts (hydrological change, eutrophication, salinisation and acidification). 4. Changes in hydrological processes, particularly the balance between groundwater-dominated versus surface water-dominated inputs and a change from seasonal to permanent water regimes appeared to be the major drivers influencing ecological regime change and the impacts of eutrophication and acidification (in urban systems) and salinisation and acidification (in agricultural systems). 5. In the absence of hydrological change, urban wetlands undergoing eutrophication and agricultural wetlands experiencing salinisation appeared to fit threshold models. Models encompassing alternative regimes and hysteresis appeared to be applicable where a change from a seasonal to permanent hydrological regime had occurred. 6. Irreversible ecological change has potentially occurred in agricultural landscapes because the external economic driver, agricultural productivity, persists independently of the impact on aquatic ecosystems. 7. Thematic implications: multiple stressors can create multiple thresholds that may act in a hierarchical fashion in shallow, lentic systems. The resulting regime shifts may follow different models and trajectories of recovery. Challenges for ecosystem managers and researchers include determining how close a system may be to critical thresholds and which processes are essential to maintaining or restoring the system. This requires an understanding of both external drivers and internal ecosystem dynamics, and the interactions between them, at appropriate spatial and temporal scales.