The construction of large water storages and subsequent alteration of flow regimes and thermal pollution have had devastating impacts on native freshwater fish populations globally. Native fish populations in the lower reaches of the Mitta Mitta River have declined substantially since the construction (in the 1970’s) and operation of Dartmouth Dam. Self-sustaining populations of Trout cod and Murray cod were reported to have substantially declined or become locally extinct in the river by the early 1990’s, attributed largely to the largely annual release of cold water during spring and summer. In more recent times, recreational fishing reports and fish surveys have detected Murray cod again occupying this reach of river. This prompted managers to reconsider the general view that the reach is unsuitable for native fish populations. Here we present outcomes of a research project aimed at improving the knowledge of the Murray cod population in the lower Mitta Mitta River with the aim of guiding improved river operations and management. We investigate patterns of population structure and hydrological records to generate a conceptual understanding of the role of water operations in influencing the current occupancy of Murray cod in the Mitta Mitta River and any interactions that may occur with Lake Hume downstream. We also present the preliminary results of an acoustic telemetry program aimed at testing our hypotheses that the altered flow and temperature regimes in the Mitta Mitta River may be influencing migratory patterns of the species.