Hydropower plays a critical role in global renewable energy production, yet its environmental impacts on aquatic ecosystems remain a concern. This study investigates the biological impacts of Shaft-Driven Variable-Speed Contra-Rotating Propeller Reversible Pump Turbines (SDCRRPTs) on fish populations, using Atlantic salmon (Salmo salar) and European eel (anguilla) as experimental models. These species present critical ecological and conservation traits, making them ideal models for assessing hydropower-induced stressors such as rapid decompression, shear, collision, and turbulence. Through Computational Fluid Dynamics (CFD) simulations and the Biological Performance Assessment (BioPA) tool, two SDCRRPT prototypes were evaluated under varying operating conditions. Results indicate that rapid decompression posed minimal risks, while shear stress was the primary cause of mortality for salmon, and collision effects were moderate but species-dependent. The optimized turbine design (Prototype 1) demonstrated improvements in adult fish passage safety compared to the initial design, particularly for eels, yet persistent vulnerabilities highlight the need for further refinements and protective measures, such as physical, mechanical or sensory behavioral barriers combined with bypass systems, to mitigate unavoidable mortality risks during turbine passage. The findings highlight the potential for species-specific design optimization to balance ecological conservation with sustainable energy production. This work underscores the importance of integrating environmental considerations into hydropower technologies to support the EU's decarbonization goals while safeguarding aquatic biodiversity.