We investigated the vulnerability of fall-spawned bull char (Salvelinus confluentus) embryos to redd scour during winter rain and rain-on-snow flood discharges in western Washington, USA. It was hypothesized that the magnitude of bedload scour at bull char redds is reduced by the provision and selection of stable refugia habitat controlled by local-, reach-, or subcatchment-scale variables such as hydraulic habitat unit and channel type. Bedload scour and channel change were measured using 96 scour monitors and 34 elevational transects in three catchments over 2 to 4 years. Scour to cited egg burial depths of bull char did not commence until discharge typically exceeded the 2-year recurrence interval. At a local scale, scour varied significantly among side channel, protected main channel, and unprotected main channel redd sites. Unprotected gravel patches in simplified channel types with moderate gradients were most susceptible to deep scour, especially if coupled with the transient supply and storage of sand and gravel from mass wasting. Partially transport-limited reaches had reduced scour due to lower stream power and armored gravel beds. Complex spawning habitat (i.e., with abundant large woody debris and side channels) was important in providing refuge from deep scour and in buffering embryos against inhospitable hydrologic or sediment regimes.