Defining stream channels in a watershed is important for assessing freshwater habitat availability, complexity, and quality. However, mapping channels of small tributary streams becomes challenging due to frequent channel change and dense vegetation coverage. In this study, we used an Unmanned Aerial Vehicle (UAV) and photogrammetry method to obtain a 3D Digital Surface Model (DSM) to estimate the total in-stream channel and channel width within grazed riparian pastures. We used two methods to predict the stream channel boundary: the Slope Gradient (SG) and Vertical Slope Position (VSP). As a comparison, the same methods were also applied using low-resolution DEM, obtained with traditional photogrammetry (coarse resolution) and two more LiDAR-derived DEMs with different resolution. When using the SG method, the higher-resolution, UAV-derived DEM provided the best agreement with the field-validated area followed by the high-resolution LiDAR DEM, with Mean Squared Errors (MSE) of 1.81 m and 1.91 m, respectively. The LiDAR DEM collected at low resolution was able to predict the stream channel with a MSE of 3.33 m. Finally, the coarse DEM did not perform accurately and the MSE obtained was 26.76 m. On the other hand, when the VSP method was used we found that low-resolution LiDAR DEM performed the best followed by high-resolution LiDAR, with MSE values of 9.70 and 11.45 m, respectively. The MSE for the UAV-derived DEM was 15.12 m and for the coarse DEM was 20.78 m. We found that the UAV-derived DEM could be used to identify steep bank which could be used for mapping the hydrogeomorphology of lower order streams. Therefore, UAVs could be applied to efficiently map small stream channels in order to monitor the dynamic changes occurring in these ecosystems at a local scale. However, the VSP method should be used to map stream channels in small watersheds when high resolution DEM data is not available.