Ecologists have examined the synchronization of population dynamics across space as a means to understand how populations respond to climate variation. However, response diversity may reflect important variation among local population dynamics driven by population-specific responses to regional environmental change. Using over 50 years of fine-scale data on sockeye salmon from pristine watersheds of southwestern Alaska, we show that populations in close proximity to one another (<40 km apart) have a limited degree of coherence in their dynamics, even after accounting for density-dependent processes (mean r = 0.45, range: 0.10 – 0.76). Of these populations, those spawning in streams flowing into a common nursery lake were substantially more coherent than populations from different lakes within the same drainage basin, suggesting some degree of synchronization at the lake scale. Using mean monthly air temperature as a predictor, we present evidence that populations within the same drainage basin respond differently to common climate conditions. The observed range of responses is likely due to fine-scale heterogeneity in spawning and rearing habitats, and adaptations of populations to this heterogeneity. Variations in life history traits, such as type of spawning habitat used, body shape and size, and age at maturity, result in diverse populations suited to a wide range of environmental conditions, and may contribute to the long-term resilience of the larger population complex. These results should guide conservation planning for Pacific salmon populations in regions where natural dynamics have been altered by habitat loss, hatchery practices, and over-fishing.