Human activities have led to the extensive modification to ecosystems and rapid decline of biodiversity globally, with freshwater ecosystems such as estuaries among the most affected. Environmental risk assessments are critical to inform ecosystem management and policy decisions, however decisions are often made on local or national scales, resulting in inconsistencies in both methodology and outcomes within and between countries. In response, the International Union for the Conservation of Nature (IUCN) Red List of Ecosystems was recently developed as a global standard for assessing the risk to ecosystems and their function. This framework has been adopted in Australia and provides a standard set of protocols for assessing the status of ecosystems and their risk of collapse against five key criteria: A) declining distribution, B) restricted distribution, C) environmental degradation, D) disruption of biotic processes or interactions, and E) quantitative modelling of the probability of ecosystem collapse. Consistent methods for selecting and applying ecological indicators to evaluate decline in ecosystem processes and functions are critical to assess ecological condition, yet current protocols remain relatively undeveloped, particularly in freshwater systems. Our research focuses on further developing approaches for 1) conceptualising and modelling ecosystem dynamics to aid indicator selection, 2) integration of multiple indicators to evaluate functional change, and 3) effective use of expert knowledge to reduce uncertainties. Our work to advance the protocols for conducting ecological risk assessments will allow for more effective management and conservation of freshwater systems.