Species-specific, flow-biotic relationships are increasingly being used to determine environmental flow needs in flow-degraded river systems. However, describing these relationships can be challenging, as other environmental variables may also influence biotic outcomes from environmental flows. This study evaluated the relationships between a range of environmental covariates and spawning intensity of an assemblage of fish using a ten-year dataset in the mid-Murray River, Australia. Our hierarchical multi-species model, that incorporated factors accounting for imperfect sampling detection, demonstrated that temperature was an important predictor of spawning intensity for all seven species studied, while both concurrent and antecedent flow conditions were important for a number of native and non-native species. This suggests that both temperature and flow influence the timing and strength of spawning for many species. We also compared the relative spawning outcomes across species using realistic alternative management scenarios; with the aim of optimising spawning outcomes for native fish, whilst reducing outcomes for non-native fish. This study highlights the benefits of long-term datasets for determining flow-biotic relationships, and demonstrates the importance of considering flow and non-flow factors in managing environmental flows.