Algal blooms produced by toxic dinoflagellates have increased worldwide, resulting in economic losses to aquaculture and fisheries. In New Zealand, the effects of paralytic shellfish poisoning (PSP) toxins on the physiology of the native scallop, Pecten novaezelandiae, are relatively unknown. Adult scallops (shell length, 94 mm) were exposed to low concentrations of the toxic PSP-producing dinoflagellate Alexandrium tamarense for 10 days followed by 8 days of depuration during which clearance rate, excretion rate, and the level of PSP toxins accumulated in the tissues were measured. For the first 6 days, scallops that had been exposed to toxic dinoflagellates had significantly lower clearance rates than the control group that was exposed to nontoxic dinoflagellates. By day 10, scallops had recovered their original clearance rate, and this rate continued throughout the depuration period. Excretion and oxygen uptake were unaffected by the PSP toxins. Differences in the toxin profile of the toxic dinoflagellates and the tissues of the scallops confirmed biotransformation of PSP algal toxins in the scallop digestive gland, where the majority of the PSP toxins were located. After 10 days of feeding on the toxic dinoflagellate, the PSP toxin level of the tissues reached 297 µg STX di-HCl equivalents/100 g. A depuration period of 8 days was insufficient to reduce the PSP toxin to safe levels (80 µg STX di-HCl equivalents/100 g) for consumption of the whole scallop.