This paper reports the development and application of two Bayesian Network models to assist decision making on the environmental flows required to maintain the ecological health of the Daly River (Northern Territory, Australia). Currently, the Daly River is unregulated, with only a small volume of water extracted annually for agriculture. However, there is considerable pressure for further agricultural development in the catchment, particularly with demand for extra water extraction during the dry season (Maya??November). The abundances of two fish speciesa??barramundi (Lates calcarifer) and sooty grunter (Hephaestus fuliginosus)a??were chosen as the ecological endpoints for the models, which linked dry season flows to key aspects of the biology of each species. Where available, data were used to define flowa??fish habitat relationships, but most of the relationships were defined by expert opinion because of a lack of quantified ecological knowledge.