In situ optical measurements of spectral absorption and beam attenuation provide information on the fine scale horizontal and vertical variations in phytoplankton pigments and other measures of phytoplankton photophysiology and ecology in coastal waters. Phytoplankton pigment ratios from discrete sample analyses with High Performance Liquid Chromatography were compared to in situ spectral absorption, hydrography, light and nutrients in protected waters in East Sound, Washington and in coastal waters off Oregon. Clear linear relationships were seen between ratios of photoprotective: photosynthetic carotenoids (PPC: PSC) and the shape of the in situ phytoplankton absorption (aph) spectra in East Sound. Linear relationships between PPC: PSC ratios and aph spectra were also found for Oregon coastal waters within groups of samples (grouped by collection date, location and temperature salinity characteristics). Inshore samples showed a similar relationship as East Sound samples. Diatoms were dominant in East Sound and Oregon shelf waters, with prokaryotes and prymnesiophytes important in Oregon waters further offshore. Environmental parameters were associated with variations in PPC: PSC ratios. Light was clearly an important factor in East Sound with a strong positive association seen between PPC: PSC ratios and recent light history. In Oregon waters, PPC: PSC ratios varied with prior light exposure, nutrients and temperature. Light exposure and temperature predicted 61% of the variability in PPC: PSC ratios for samples with low nutrients (dissolved inorganic nitrogen <2 μ M). In situ optical measurements indicated considerable spatial variation in phytoplankton photophysiology and taxonomic composition in the Oregon costal region. Phytoplankton assemblages often had lower PPC: PSC ratios, flatter particle size distributions slopes suggesting greater contributions by large particles, higher chlorophyll a per particle, and more packaging in the nutrient-rich upwelled waters near shore compared to further offshore. These results indicate that in situ measurements of spectral absorption and beam attenuation can predict PPC: PSC ratios and other photophysiological and taxonomic indices in coastal waters. Such data provide high-resolution information on phytoplankton characteristics on the same temporal and spatial scales as physical properties such as temperature and salinity, and offer important insights into light history and the transfer of absorbed light within phytoplankton cells
