In light of Switzerland’s 2050 energy goals, the nation aims to boost its domestic hydroelectric output, notably focusing on small-scale hydroelectric power plants. Concurrently, there is an effort to renovate hydroelectric plants to make them more environmentally friendly, emphasizing ecological flow regulation to improve river conditions. This study explores the application of a non-proportional flow allocation method to better assess both ecological and economic outcomes. Unlike traditional fixed or proportional flow methods, this approach allows for a more dynamic balance between hydropower generation and riverine ecosystem health. This study focuses on two key species, brown trout and grayling. In particular, this work highlighted that trout are better suited for low-flow conditions (Weighted Usable Area, WUA, peaks below 1 m3/s), while grayling require significantly higher flows (WUA peaks over 4.5 m3/s). This disparity in habitat preferences raises concerns about the current reliance on single-species models, emphasizing the need for multi-species ecological assessment in future studies. When applied to a small hydropower plant in the Swiss Jura, the non-proportional flow method resulted in an improvement of ecological conditions of at least 37.7%, which consequently led to a reduction of the hydroelectric production of at least 10%. Through strategic upgrades to the facility (e.g., by minimizing hydraulic losses, implementing more efficient turbines, or incorporating photovoltaic panels over water channels), it is possible to simultaneously enhance both energy output and environmental sustainability. These findings suggest that non-proportional flow allocation holds significant potential for broader use in sustainable hydropower management, providing a pathway toward meeting both energy production and ecological conservation goals.