Cold water pollution is a critical bottleneck to the successful spawning and recruitment of native fish in the Murray-Darling Basin. This study presents historical NSW Fisheries survey data dating back to 1999 to examine recruitment trends in four large-bodied native fish species in rivers affected by cold water pollution. The fish communities were dominated by larger, older individuals, with minimal numbers of young-of-year fish and no recruitment events of note evident among the species present. The lack of recruitment was consistent despite extensive stocking efforts and suitable spawning temperatures being reached annually. The results of our study indicate the combined influence of cold-water pollution, frequent rapid fluctuations in temperature (or cold shock), and flow regulation are having a profound effect on the population dynamics of native fish. Our findings underscore the substantial impact of dam operations on river thermal regimes and fish populations, highlighting the urgent need for adaptive management strategies to mitigate these ecological challenges.