Freshwater environments provide different ecosystem services for human well-being, and are one of the most important natural sources of healthy animal protein. Climate change and extreme temperature events, among other factors, represent a growing concern for their sustainable use. In contrast to the research effort to elucidate how global warming affects these aquatic environments, few studies pay attention to the potential effects of heat waves, a current phenomenon with direct effects on contemporaneous organisms. Here, the potential effects of a single heat wave event on rainbow trout (Oncorhynchus mykiss) males, mimicking a recorded environmental event, have been evaluated by means of biometric, redox and stress response, plasma testosterone, histopathology and transcriptomic analyses. Environmental monitoring showed how, during the last 4 years, mean water temperature increased (2–4 °C; from April to October), heat wave duration progressively increased (from 15 to 100 days), and mean intensities ranged 1.7–3.8 °C with a maximum of 8.0 °C. An experimentally recreated heat wave lasting only 16 days, with mean and maximum intensities of 2.7 and 6.7 °C, induced a decrease in body weight and total antioxidant status, but increased blood plasma cortisol levels and redox enzyme activity. The induced heat wave decreased testosterone plasma levels and sperm quality, arrested spermatocyte type I and II differentiation and increased spermatozoa apoptosis. These effects were correlated with a differential expression of 1156 genes (116 up- and 1040 down-regulated genes) in exposed fish when compared to Control fish, reflecting an alteration in cell apoptosis and spermatozoa maturation processes. These results not only increase concern about current heat wave events, recreating a real scenario, but also unveil for the first time the particular molecular mechanisms of subsequent spermatogenesis disruption, opening new avenues for designing urgent and necessary strategies to mitigate the effects of extreme climate change conditions on freshwater aquaculture.