<p><strong>Abstract.</strong> Phytoplankton taxonomy, pigment composition and photo-physiological state were studied in Galveston Bay (GB), Texas (USA) following the extreme flooding associated with Hurricane Harvey (August 25&ndash;29, 2017) using field and satellite ocean color observations. Percentage of chlorophyll a (Chl a) in different phytoplankton groups were determined from a semi-analytical IOP (inherent optical property) inversion algorithm. The IOP inversion algorithm revealed the dominance of freshwater species (cyanobacteria and green algae) in the bay following the hurricane passage (September 29, 2017) under low salinity conditions associated with the discharge of floodwaters into GB; 2 months after the hurricane (October 29&ndash;30, 2017), under more seasonal salinity conditions, the phytoplankton community transitioned to an increase in small sized groups such as haptophyte and prochlorophyte. Sentinel-3A OLCI-derived Chl a obtained using a red/NIR band ratio algorithm for the turbid estuarine waters was highly correlated (R<sup>2</sup> > 0.90) to HPLC-derived Chl a concentrations. A Non-Negative Least Square (NNLS) inversion model was then applied to OLCI-derived Chl a maps of GB to obtain spatiotemporal distributions of phytoplankton diagnostic pigments; results appeared consistent with extracted phytoplankton taxonomic composition derived from the IOP inversion algorithm. OLCI-derived diagnostic pigment distributions also exhibited good agreement with HPLC measurements, with mean R<sup>2</sup> ranging from 0.39 for violaxanthin to 0.98 for Chl a. Environmental factors (e.g. floodwaters) combined with phytoplankton taxonomy also strongly modulated phytoplankton physiology in the bay as indicated by measurements of photosynthetic parameters with a Fluorescence Induction and Relaxation (FIRe) system. Phytoplankton in well-mixed waters (mid-bay area) exhibited maximum PSII photochemical efficiency (F<sub>V</sub>/F<sub>M</sub>) and low effective absorption cross section (&delta;<sub>PSII</sub>), while the areas adjacent to the shelf (likely nutrient-limited) showed low F<sub>V</sub>/F<sub>M</sub> and elevated values. Overall, the approach using field and ocean color data combined with inversion models allowed, for the first time, an assessment of phytoplankton response to a large hurricane-related floodwater perturbation in a turbid estuarine environment based on its taxonomy, pigment composition and physiological state.</p>