The modern integrated fish-seaweed mariculture has been tested to reduce the environmental impacts of an intensive fed culture. To obtain the best seaweed bioremediation performance, the effects of therapeutants used for fish disease control on the selected seaweed species should be considered. As a selected seaweed, Porphyra yezoensis was tested with six commercial antibiotics including erythromycin thiocyanate_A, erythromycin thiocyanate_B, oxytetracycline, doxycycline, pefloxacin, and amoxicillin trihydrate under the batch incubation at a photon flux density of 10 $mu$mol ${cdot}m^{-2};{cdot};s^{-1}$ at 15$^{circ}C$. Among the tested commercial antibiotics, erythromycin thiocyanate_A, erythromycin thiocyanate_B, oxytetracycline, and doxycycline showed decreases in Fv/Fm, the photochemical efficiency of photosystem II, with a dose-dependant and time-dependant manner. From the quenching analysis of chlorophyll fluorescence, three differential patterns were observed in the antibiotics-treated Porphyra: (1) high nonphotochemical quenching (NPQ) and low photochemical quenching (qP) in the cases of Erythromycin thiocyanate_B and amoxicillin trihydrate, (2) high NPQ and high qP in the case of pefloxacin and (3) low NPQ and low qP in the case of oxytetracycline. These results indicated that antibiotics affected in various ways on the photosynthetic apparatus, reflecting differential lesion sites of antibiotics. In addition, the rates of ammonium uptake also decreased with a decrease of Fv/Fm in P. yezoensis thalli treated with erythromycin thiocyanate_B and oxytetracycline. Therefore, the four antibiotics mentioned could affect the bioremediation capacity of the selected seaweed species in the integrated fish-seaweed mariculture system due to the decrease of photosynthetic activity and the simultaneous decrease of ammonium uptake.