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Surface-canopy forming kelps ( Macrocystis pyrifera and Nereocystis luetkeana ) can be monitored along the Northeast Pacific coast using remote sensing. These kelp canopies can be submerged by tides and currents, making it difficult to accurately determine their extent with remote sensing techniques. Further, both species have morphologically distinct canopies, each made up of structures with differing buoyancies, and it is not well understood whether the differing buoyancies between these species’ canopies affects their detectability with remote sensing technologies. Here, we collected in situ above-water spectral signatures for the surface-canopies of Nereocystis and Macrocystis , providing the first direct hyperspectral comparison between the structures that make up the canopies of these species. Additionally, we compare the strength of their red-edge and near-infrared band signals, as well as the normalized difference red-edge (NDRE) and normalized difference vegetation index (NDVI) values. At the bed level, we compare detection of kelp canopy extent using both NDRE and NDVI classified unoccupied aerial vehicle imagery. We also characterized how changing tides and currents submerge the canopies of both species, providing insights that will allow remote sensors to more accurately determine the extent of kelp canopy in remote sensing imagery. Observations of canopy structures paired with in situ hyperspectral data and simulated multispectral data showed that more buoyant kelp structures had higher reflectance in the near-infrared wavelengths, but even slightly submerged canopy structures had a higher reflectance in the red-edge rather than the near-infrared. The higher red-edge signal was also evident at the bed level in the UAV imagery, resulting in 18.0% more canopy classified with NDRE than with NDVI. The area of detected canopy extent decreased by an average of 22.5% per meter of tidal increase at low current speeds (<10 cm/s), regardless of the species present. However, at higher current speeds (up to 19 cm/s), Nereocystis canopy decreased at nearly twice the average rate of kelp beds in low-current conditions. Apart from the strong differences in high-current regions, a robust linear relationship exists between kelp canopy extent and tidal height, which can aid in understanding the errors associated with remote sensing imagery collected at different tidal heights.