Abstract Summer water temperatures within many temperate rivers regularly surpass the incipient lethal temperature for juvenile Atlantic salmon (c. 27°C), causing widescale abandonment of territory in favour of areas of cooler water (thermal refuges). This study aims to highlight the influence of thermal refuges on river‐scale abundance patterns. That is, do salmon parr adjust their distribution over time according to proximity to thermal refuges? Twelve reaches (seven reference: five refuge) were chosen along a 17‐km section of the Little Southwest Miramichi River in Canada. Reaches were sampled throughout the 2011 and 2012 summer periods; high temperature events were recorded during summer 2012 but not summer 2011. Multivariate principal component analyses indicated no discernible difference in habitat characteristics between the reach‐types under normal thermal conditions. However, reaches containing a thermal refuge had a significant increase in relative abundance of parr immediately after a series of high temperature events (water temperature >26°C) in 2012 (p = 0.034). This increase in relative abundance in refuge reaches was not present during the summer of 2011 when no temperature events occurred (p = 0.088), prior to the event of 2012 (p = 0.999), or at the late autumn survey following the 2012 event (p = 0.999). Difference in temperature between refuge and mainstem reaches significantly influenced the suitability of a tributary as a thermal refuge habitat (R2 = 0.84), with preference shown for cooler refuges. River‐wide thermal heterogeneity therefore plays a critical role in survival of juvenile salmon throughout summer months and is likely to become necessary under future climate change scenarios.