Continuous, high-resolution data for characterizing freshwater habitat conditions can support successful management of endangered salmonids. Uncrewed aircraft systems (UAS) make acquiring such fine-scale data along river channels more feasible, but workflows for quantifying reach-scale salmon habitats are lacking. We evaluated the potential for UAS-based mapping of hydraulic habitats using spectrally based depth retrieval and particle image velocimetry (PIV) by comparing these methods to a more well-established flow modeling approach. Our results indicated that estimates of water depth, depth-averaged velocity, and flow direction derived via remote sensing and modeling techniques were comparable and in good agreement with field measurements. Predictions of spring-run Chinook salmon (Oncorhynchus tshawytscha) juvenile rearing habitat produced from PIV and model output were similar, with small errors relative to direct field observations. Estimates of hydraulic heterogeneity based on kinetic energy gradients in the flow field were generally consistent between PIV and flow modeling, but errors relative to field measurements were larger. PIV results were sensitive to the velocity index (α) used to convert surface velocities to depth-averaged velocities. Sun glint precluded PIV analysis along the margins of some images and a large degree of overlap between frames was thus required to obtain continuous coverage of the reach. Similarly, shadows cast by riparian vegetation caused gaps in spectrally based bathymetric maps. Despite these limitations, our results suggest that for sites with sufficient water surface texture, UAS-based PIV can provide detailed hydraulic habitat information at the reach scale, with accuracies comparable to traditional field methods and multidimensional flow modeling.