We investigated physical habitat conditions associated with the spawning sites of Chinook Salmon Oncorhynchus tshawytscha and the interannual consistency of spawning distribution across multiple spatial scales using a combination of spatially continuous and discrete sampling methods. We conducted a census of aquatic habitat in 76 km of the upper main-stem Yakima River in Washington and evaluated spawning site distribution using redd survey data from 2004 to 2008. Interannual reoccupation of spawning areas was high, ranging from an average Pearson’s correlation of 0.62 to 0.98 in channel subunits and 10-km reaches, respectively. Annual variance in the interannual correlation of spawning distribution was highest in channel units and subunits, but it was low at reach scales. In 13 of 15 models developed for individual years (2004–2008) and reach lengths (800 m, 3 km, 6 km), stream power and depth were the primary predictors of redd abundance. Multiple channels and overhead cover were patchy but were important secondary and tertiary predictors of reach-scale spawning site selection. Within channel units and subunits, pool tails and thermal variability, which may be associated with hyporheic exchange, were important predictors of spawning. We identified spawning habitat preferences within reaches and channel units that are relevant for salmonid habitat restoration planning. We also identified a threshold (i.e., 2-km reaches) beyond which interannual spawning distribution was markedly consistent, which may be informative for prioritizing habitat restoration or conservation. Management actions may be improved through enhanced understanding of spawning habitat preferences and the consistency with which Chinook Salmon reoccupy spawning areas at different spatial scales.