The rivers of the Queensland Murray-Darling Basin experience wide variation in hydrology, and hence ecology, such as fish habitat and stream biogeochemistry (BGC). Hydrologic extremes create productive lowland floodplains during floods, and isolated waterholes during prolonged dry periods. Waterholes can support aquatic biota until water quality conditions no longer allow, or when the next flow pulse connects waterholes with water and resources. As global change pushes systems beyond historical climate and hydrologic norms, water quality in isolated water holes is degrading, and threats to native fish populations increase. The State of Queensland is exploring new methods for assessing risks to native fish to inform sustainable water planning. To aid in the assessment, we are developing an integrated modelling framework to simulate waterhole ecohydrology and examine how waterhole characteristics and surrounds affects water quality and habitat. The model will be used to estimate habitable volume for different fish species from dissolved oxygen, temperature, and novel fish physiology research that has shed light on responses to low dissolved oxygen. In addition to conventional methods of validation for BGC models, which leverage values of state variables to demonstrate model fitness, we propose to evaluate the underlying processes controlling water quality conditions, namely stream metabolism. Stream metabolism is the balance of carbon and oxygen in the water column, and is comprised of two general components: gross primary production (GPP) from algae, aquatic plants and photosynthetic bacteria; and ecosystem respiration (ER) from all aquatic biota. We present the model parameterization results, including its validation against selected variables of state (temperature and dissolved oxygen) and relevant fluxes (GPP and ER). We also discuss the implications of the research with regard to setting EFOs.