The concepts of ecosystem regime shifts, thresholds and alternative or multiple stable states are used extensively in the ecological and environmental management literature. When applied to aquatic ecosystems, these terms are used inconsistently reflecting differing levels of supporting evidence among ecosystem types. Although many aquatic ecosystems around the world have become degraded, the magnitude and causes of changes, relative to the range of historical variability, are poorly known. A working group supported by the Australian Centre for Ecological Analysis and Synthesis (ACEAS) reviewed 135 papers on freshwater ecosystems to assess the evidence for pressure-induced non-linear changes in freshwater ecosystems; these papers used terms indicating sudden and non-linear change in their titles and key words, and so was a positively biased sample. We scrutinized papers for study context and methods, ecosystem characteristics and focus, types of pressures and ecological responses considered, and the type of change reported (i.e., gradual, non-linear, hysteretic or irreversible change). There was little empirical evidence for regime shifts and changes between multiple or alternative stable states in these studies although some shifts between turbid phytoplankton-dominated states and clear-water, macrophyte-dominated states were reported in shallow lakes in temperate climates. We found limited understanding of the subtleties of the relevant theoretical concepts and encountered few mechanistic studies that investigated or identified cause-and-effect relationships between ecological responses and nominal pressures. Our results mirror those of reviews for estuarine, nearshore and marine aquatic ecosystems, demonstrating that although the concepts of regime shifts and alternative stable states have become prominent in the scientific and management literature, their empirical underpinning is weak outside of a specific environmental setting. The application of these concepts in future research and management applications should include evidence on the mechanistic links between pressures and consequent ecological change. Explicit consideration should also be given to whether observed temporal dynamics represent variation along a continuum rather than categorically different states.