In regulated rivers, hydropeaking operations have been identified as having significant effects on spawning, growth, reproduction, and behavior of juvenile salmonids. Such effects may reduce survival rates and population viability, but such long-term studies are challenging. Due to the inherent difficulties of conducting large-scale replicated studies in such regulated rivers in situ, river managers require new tools to assess how mitigation measures may affect fish populations. In this study, we used inSALMO 7.3-SD, an individual-based model developed for hydropeaking studies, to investigate the effects of three levels of minimum baseflows (9, 12 and 15 m3/s) and spawning gravel augmentation on the size and number of Atlantic salmon (Salmo salar) and brown trout (S. trutta) outmigrants in the hydropeaking-regulated River Gullspång, Sweden. Our results show that under hydropeaking conditions, higher minimum flows increased outmigrant size, they simultaneously reduced outmigrant numbers, affecting age-1 trout and age-2 individuals of both species. In contrast, gravel augmentation did not affect outmigrant size but generally increased outmigrant production, mainly benefiting age-1 salmon and age-2 trout, although this effect diminished at higher base flow levels. We identified poor body condition and fish predation of juveniles as the primary mortality sources driving the effects on outmigrant production. Our results indicate that the spatial distribution of juveniles was affected by gravel addition and that this effect in turn led to altered mortality rates. Our findings underscore the complex interplay between flow management, habitat modifications, and species-specific behaviors. Also, they highlight the need to carefully balance operational and morphological restoration measures to optimize habitat quality and support effective conservation of salmonids in hydropeaking-regulated rivers.