Two of the biggest challenges in terms of environmental-flow management are deciding what ecological characteristic to measure and then detecting whether the flow restoration had the desired impact. We used a “gradient analysis” to identify a subset of environmental indicators that respond predictably to environmental flow-disturbance gradients in the Murray-Darling Basin. Four types of potential indicators were calculated using the Sustainable Rivers Audit data and used to assess medium-term responses to managed-flow regimes: fish abundance, biomass, recruit count, and Fulton’s body condition. Potential indicators were calculated for four species, including two native species and two exotic species. These potential indicators were assessed using 33 flow-disturbance metrics representing the raw, percent, and absolute change in modelled flow variability, magnitude, frequency, duration, timing, and inundation frequencies between pre- and post-development time periods. Other environmental variables such as mean annual temperature or elevation were used to account for natural variability in fish distribution, while distance-weighted land-use measures were used to account for land-use type and proximity to streams and perennial waterbodies. We were able to successfully identify and quantify a number of relationships between potential indicators and flow-disturbance gradients. We found that 1) traditional indicators of ambient condition may not be suitable as indicators of flow alteration, 2) indicators will likely be species specific and native species may be more suitable than exotic species, and 3) it may be important to use region-specific indicators if climatic conditions vary substantially or species have evolved region-specific life-history characteristics.