Employing Baikal sculpins (Cottoidei) as model organisms, this study simulated the effects of human-induced rapid environmental change (HIREC) to experimentally test the novel hypothesis of sex-specific responses to chronic noise exposure in fish. In the stone sculpin (Paracottus knerii Dybowski, 1874), a species of Baikal sculpin, long-term exposure to noise at mean sound pressure levels of 160–179 dB re 1 μPa (SPL peak-to-peak) resulted in sexually dimorphic physiological responses. Females exhibited signs of excessive stress, whereas males demonstrated adaptive recalibrations. This divergence is potentially attributable to the unique paternal offspring care strategy and the distinct biological role males fulfill in the reproductive behavior of this species. The findings illuminate the interconnections between HIREC-associated noise pollution and long-term, sex-linked physiological alterations, with implications for predicting a species’ evolutionary trajectory. Such modeling of HIREC scenarios not only forecasts potential anthropogenic impacts but also serves to uncover innate, sex-linked mechanisms of stress resistance, thereby informing the development of more effective environmental management and conservation strategies.