The thermal regime of rivers plays a key role in aquatic ecosystem health. In the Willamette River, OR, main channel temperatures can be too warm for cold water fishes, causing fish to concentrate in secondary channel features including side channels, ponds, and alcoves. However, temperature regimes vary among and within features. Improved understanding of physical processes controlling thermal regimes in gravel-bed rivers is needed for targeted conservation action. This study characterized thermal regimes on the Willamette through field observations of temperature continuously measured at one side channel, eight alcoves, and six beaver ponds over a two month period. Insight into these measurements was provided by two dimensionless quantities. The Richardson number, characterizing stratification, was calculated with temperature and flow data. Values showed two well-mixed sites and 13 stratified sites. Stratification allowed calculation of the hyporheic-insolation number, characterizing the ratio of cooling flux from hyporheic discharge to heat transfer from incoming solar radiation. As calculated hyporheic-insolation numbers for sites increased, measured temperatures at sites decreased, showing a bin-averaged logarithmic fit R2=0.97. Results further indicate secondary channel features that provide cold water habitat are characterized by stratification and cool hyporheic discharge. Stratification is a necessary yet insufficient condition for cold water to provide habitat for aquatic biota because cold areas may still be anoxic, as suggested by dissolved oxygen point measurements. The hyporheic-insolation number has the ability to predict and thereby classify the thermal regimes of secondary channel features based on minimal field measurements and could guide floodplain restoration efforts.