It is demonstrated that hyperspectral imagery can be used, without atmospheric correction, to determine the presence of accessory phytoplankton pigments in coastal waters using derivative techniques. However, care must be taken not to confuse other absorptions for those caused by the presence of pigments. Atmospheric correction, usually the first step to making products from hyperspectral data, may not completely remove Fraunhofer lines and atmospheric absorption bands and these absorptions may interfere with identification of phytoplankton accessory pigments. Furthermore, the ability to resolve absorption bands depends on the spectral resolution of the spectrometer, which for a fixed spectral range also determines the number of observed bands. Based on this information, a study was undertaken to determine under what circumstances a hyperspectral sensor may determine the presence of pigments. As part of the study a hyperspectral imager was used to take high spectral resolution data over two different water masses. In order to avoid the problems associated with atmospheric correction this data was analyzed as radiance data without atmospheric correction. Here, the purpose was to identify spectral regions that might be diagnostic for photosynthetic pigments. Two well proven techniques were used to aid in absorption band recognition, the continuum removal of the spectra and the fourth derivative. The findings in this study suggest that interpretation of absorption bands in remote sensing data, whether atmospherically corrected or not, have to be carefully reviewed when they are interpreted in terms of photosynthetic pigments.