A decision to develop mineral resources within unregulated, ephemeral surface water catchments of the Lake Eyre Basin requires a proper assessment of social, economic and environmental risks within the socio-political context of the day. But, how do decision-making authorities properly assess and make an informed decision on a mining proposal without a way to incorporate ecological complexity into their risk assessments? This presentation outlines data gathering, analyses and modelling currently being trialled to aid future decision-makers in exploring hydro-ecological risks that alternate decision and management scenarios present for aquatic ecosystem ‘agents’ (represented by four native fish species) and ‘domains’ (represented by defined aquatic ecosystem function zones) in the Arckaringa Basin in Northern South Australia. Our experience shows that developing a useful decision support model (DSM) requires a consultative process to understand the context of regulatory needs and uncertainty. We discuss options for DSMs that allow managers and decision-making authorities to openly explore priorities and risk criteria setting for highly valued but lesser known aquatic ecosystems of Lake Eyre Basin Rivers.