Harmful algal blooms (HAB) may impose a serious threat to aquatic lives and human health. We determined the effects of a toxic dinoflagellate Alexandrium tamarense (clone ATCIO1, isolated from Hong Kong coastal waters) on the energy budget, quantified as scope for growth (SFG), and the growth rate of the manila clam Ruditapes philippinarum and the green-lipped mussel Perna viridis. To quantify the SFG, clams and mussels were dosed with different amounts of toxic A. tamarense for 6 days, resulting in different toxin burdens in the tissues. Clearance rate, absorption efficiency, and respiration rate were subsequently measured in these toxin containing bivalves. Clearance rate significantly declined at the highest toxin burden in the clams only, while there was no significant difference in the clearance rate among different treatments for the mussels. The respiration rate of either bivalve was not significantly affected by toxin accumulation in the tissues. In contrast, the absorption efficiency of both clams and mussels decreased, in a concentration-dependent manner for mussels but not for clams, when the tissue accumulated the toxins. With an increase in paralytic shellfish poisoning (PSP) toxin burden, SFG in both clams and mussels was significantly reduced, primarily because of the decrease of absorption efficiency. The growth rate of juvenile clam R. philippinarum, measured as an increment in tissue dry weight over a 15 d exposure period, was significantly lower during their feeding on toxic dinoflagellate than the growth rate of clams feeding on the diatom Thalassiosira pseudonana. The juvenile mussel P. viridis, however, exhibited similar growth rates after feeding on the toxic dinoflagellates and the nontoxic diatom. This study showed that SFG can provide a sensitive and integrated measure of the effect of HAB on the physiology of bivalves. Clam R. philippinarum may be more sensitive, in terms of their energy budget, to PSP toxin accumulation than the mussel P. viridis.