Green seawater discolorations caused by the marine dinoflagellate Lepidodinium chlorophorum are frequently observed during the summer along the southern coast of Brittany, France. Although there is no evidence that L. chlorophorum produces toxins, green seawater discolorations are related to mortalities of filter feeding animals. Here, we investigate the ecophysiological response of the Pacific oyster Crassostrea gigas exposed to L. chlorophorum. Oysters were exposed for 48 h to a low concentration (500 cells mL−1) and a bloom concentration (7500 cells mL−1) of L. chlorophorum and compared to controls fed with the haptophyte Tisochrysis lutea. The direct consequences of L. chlorophorum exposure were assessed through semiquantitative histochemical analysis. Thereafter, a 24 h-recovery phase with a diet based on T. lutea was studied using an individual ecophysiological measurement system. We found that oysters successfully filtered L. chlorophorum cells with increased mucus secretion in all tissues analyzed. Animals previously exposed to a bloom concentration of L. chlorophorum exhibited significantly lower clearance rates shortly after the exposition, probably reflecting the effect of exopolymer particles produced by L. chlorophorum cells, and the subsequent production of mucus in the mantle and gills. However, their absorption efficiency was two-fold higher than control oysters exposed to T. lutea. The increase in absorption efficiency during the recovery phase could be a compensation for a decrease of clearance rate occurred during the exposure phase, interpreted as physiological depletion of C. gigas during green seawater discolorations. For the first time, laboratory experiments showed how high concentrations of L. chlorophorum can affect oyster physiology.