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Chlorophyll fluorescence measurements provide valuable information on phytoplankton abundance and physiology. High spectral resolution measurements from the aircraft-mounted Portable Remote Imaging SpectroMeter (PRISM) allow for a more robust and informative fluorescence measurement than previous methods. An increase in radiation in the fluorescence wavelength range is approximated by a skew-normal distribution. Positive skew suggests the influence of water attenuation and motivates the use of an inverse retrieval model to solve for the most likely vertical distribution of fluorescence quantum yield. This approach is tested with theoretical fluorescence profiles and applied to a PRISM flightline located in southern Drake Passage, Southern Ocean during austral summer. The resulting profiles suggest vertical structure in fluorescence quantum yield in the upper 10 m, which matches expectations from in situ studies. The framework developed in this paper can be applied to current and future satellite missions, providing more information on phytoplankton concentrations, vertical profiles, and physiology.

Plain Language Summary When chlorophyll molecules absorb light in the visible wavelengths, part of the energy is released in the form of light (fluorescence) in far-red and near-infrared wavelengths. Measurements of this fluorescence provide an independent estimate of the amount of photosynthesis occurring in the water, compared with other methods related to measuring the absorption of light by chlorophyll. Importantly, the theoretical "spectral shape," or the amount of light released at each wavelength, of fluorescence is well known. Here we report measurements of the spectral shape of fluorescence in the ocean from aircraft measurements. The actual spectral shape is different from theoretical expectations. However, fluorescence emanating from chlorophyll at shallow depths (less than 10 m) is modified by interactions with the water column above it, leading to differences in the spectral shape observed by aircraft. We use an algorithm that finds the vertical profile of fluorescence in the ocean that best matches the observations. This best match corresponds to a subsurface maximum in fluorescence, consistent with common profiles measured in situ.