Small hydropower plants (SHP) are vital for sustainable energy generation in remote mountainous regions however their performance is often constrained by fluctuating hydrological conditions sedimentation and limited operational flexibility. This study evaluated the performance of representative run-of-river SHP plants in high-altitude Himalayan and Alpine terrains under variable flow conditions using a combined empirical and simulation-based approach. Six SHP sites were monitored between 2018 and 2023 to assess flow variability head fluctuation and sediment-induced efficiency losses. Statistical analyses including regression and paired-sample comparisons were employed to determine the relationship between flow variability and performance deviation from design capacity. Results showed that the capacity utilization factor (CUF) under conventional fixed-speed operation averaged between 0.22 and 0.39 substantially lower than the design benchmark of 0.45. Flow coefficient of variation and sediment load were identified as dominant predictors of performance loss explaining most of the variance in energy shortfall across sites. Variable-speed and staged turbine operations demonstrated significant improvements in both efficiency and annual energy output achieving average gains of 11-13% and 7-9% respectively. The hybrid empirical-simulation model achieved strong predictive accuracy (R² > 0.9) validating its suitability for mountainous SHP performance assessment. The study concludes that adaptive operational strategies can substantially mitigate flow-related inefficiencies without extensive civil modifications. Practical recommendations include integrating variability-aware design real-time flow control systems modular turbine configurations and advanced sediment management to improve operational resilience. The findings underscore the need for hydrologically responsive design frameworks and adaptive control technologies to enhance the sustainability and reliability of small hydropower plants in mountainous regions.