Abstract Increased flood magnitude and frequency due to climate change can reduce the population productivity of organisms such as amphibian and fish species in river and stream systems; therefore, conserving habitats that maintain high productivity under such conditions is crucial. Here, we examined the relationship between the freshwater productivity of anadromous salmonids (measured as fry migrating to the ocean per spawner) and catchment hydrogeomorphology and identified the characteristics of rivers and streams that are prone to flood disturbance. We surveyed the spawner abundance and number of fry of pink salmon (Oncorhynchus gorbuscha) and measured environmental factors, including the average catchment slope and stream power, as characteristics of hydrogeomorphology, in 10 streams in the Shiretoko Peninsula, northern Japan. We then used generalised linear mixed models to predict the freshwater productivity of pink salmon populations in each catchment across the study region under current and future climatic conditions. The productivity of pink salmon in the study region differed among the sampled catchments and was negatively affected by the average catchment slope, stream power, and maximum daily precipitation averaged over the catchment. Namely, flood disturbance reduced the freshwater productivity of pink salmon, and salmon productivity in individual catchments was explained by catchment hydrogeomorphology. The predicted future productivity with increased precipitation was also lower than the current productivity. Our approach can be applied to other salmonids that have similar spawning behaviour to pink salmon. Highly productive catchments under the future climatic conditions predicted by the present study should be prioritised for conservation to ensure a sustainable salmonid population.