Under laboratory conditions, the scallop Chlamys nobilis and the mussel Perna viridis were exposed to N-sulfocarbamoyl toxins (C2 toxin), a paralytic shellfish toxin (PST), by feeding a local toxic strain of the dinoflagellate Alexandrium tamarense (ATDP) that produced C2 toxin exclusively. The bivalves were subsequently depurated in the field, and their depuration kinetics, biotransformation and toxin distribution were quantified. Depuration was characterized by a rapid loss within the first day, followed by a secondary slower loss of toxins. In the fast depuration phase, scallops detoxified PSTs more quickly than the mussels (depuration rate constants for scallops and mussels were 1.16 day−1 and 0.87 day−1, respectively). In contrast, the mussels detoxified PSTs more quickly than the scallops in the slow depuration phase, and the calculated depuration rate constants (mean+SE) from day 2 to day 13 were 0.063+0.009 day−1 and 0.040+0.019 day−1 for mussels and scallops, respectively. The differences in the appearances of gonyautoxins, GTX2 and GTX3, and their decarbamoyl derivatives, dcGTX2, dcGTX3 and GTX5, which are all derivatives of C2 toxin, indicated active and species-specific biotransformation of the algal toxins in the two bivalves. In both species of bivalves, the non-viscera tissue contained fewer toxins and lower concentrations than the viscera-containing tissue compartment. In scallops, very little toxin was distributed in the adductor muscle. In mussels, most of the PSTs were found in the digestive gland with significant transport of toxins into the digestive gland from other tissues during the course of depuration. The toxin profiles of scallops and mussels differed from each other and from that of the toxic algae fed. A significant fraction of GTX5 was detected in the mussels but not in the scallops. Our study demonstrates a species specificity in the depuration kinetics, biotransformation and tissue distribution of PSTs among different bivalves.