Combining single-species ecological modeling with advanced machine learning to investigate the long-term population dynamics of the rheophilic fish spirlin offers a powerful approach to understanding environmental changes and climate shifts in aquatic ecosystems. A new ESHIPPOClim model was developed by integrating climate change assessment into the ESHIPPO model. The model identifies spirlin as a potential early indicator of environmental changes, highlighting the interactive effects of climate change and anthropogenic stressors on fish populations and freshwater ecosystems. The ESHIPPOClim model reveals that 28.57 % of the spirlin's data indicates high resilience and ecological responsiveness, with 34.92 % showing medium-high adaptability, suggesting its substantial ability to withstand environmental stressors. With 36.51 % of the data in medium level and no data in the low category, spirlin may serve as a sentinel species, providing early warnings of environmental stressors before they severely impact other species or ecosystems. The results of uniform manifold approximation and projection (UMAP) and a decision tree show that pollution has the highest impact on the population dynamics of spirlin, followed by annual water temperature, overexploitation, and invasive species. Despite the obtained key drivers, higher abundance, dominance, and frequency values were detected in habitats with higher HIPPO stressors and climate change effects. Integrating state-of-the-art machine learning models has enhanced the predictive power of the ESHIPPOClim model, achieving approximately 90 % accuracy in identifying spirlin as an early indicator of climate change and anthropogenic stressors. The ESHIPPOClim model offers a holistic approach with broad practical applications using a simplified three-point scale, adaptable to various fish species, communities, and regions. The ecological modeling supported with advanced machine learning could serve as a foundation for rapid and cost-effective management of aquatic ecosystems, revealing the adaptability potential of fish species, which is crucial in rapidly changing environments.