River impoundment affects ecological communities through changes in downstream physical, chemical and biological processes. Fish species within these communities are impacted largely by changes in thermal regimes and flow alteration. These changes modify micro and meso-scale habitat suitability, trophic resource availability and thermally-regulated physiological processes such as metabolic rate, thermal tolerance and reproductive timing. While the impacts of river impoundment on large-bodied fish have received broad attention in the literature, less research has been directed toward impacts on small-bodied fish species. To better understand how river impoundment impacts Australian native small-bodied fish populations, this research will employ stable isotope analysis (δ13C and δ15N) to quantify basal carbon sources, energy pathways and trophic structure in northern Murray-Darling Basin river systems with and without river impoundment. Isotopic data and stocking records will also be used to infer potential competition and predation between natal and stocked species such as Murray cod and Golden perch. Downstream physical habitat characteristics, and how these are altered by river impoundment, will be investigated using habitat complexity metrics. Additionally, this project will investigate the efficacy of cold-water pollution mitigation measures such as the bubble plume system recently installed in Pindari Dam on the Severn River, NSW, which offers promising options for remediation of downstream ecological communities. This project forms part of the Commonwealth Environmental Water Holder’s Flow Monitoring Evaluation Research (Flow-MER) program for the Border Rivers, Barwon and Namoi selected area, a collaboration between Griffith University, La Trobe University, and NSW Fisheries. Here we provide an overview and background for the project with fieldwork commencing in late 2026.