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We aimed to identify functional differences between different sections of the thallus of <i>Ulva australis</i> and develop tissue-endpoint combinations to assess the toxicity of six metals (i.e., Ag, As, Cd, Cr, Cu, and Ni). EC₅₀ values for these metals in three sections of the thallus of <i>Ulva</i> were obtained for multiple endpoints: relative growth rate (RGR), chlorophyll <i>a</i> fluorescence, pigment contents, and the expression of the photosynthesis-related gene, <i>rbcL</i>. The responses of the endpoints varied across the respective thallus sections; overall, the most toxic metals were Ag and Cu. These endpoints were the best for evaluating metal toxicity: ETR_max of the middle thallus sections for Ag toxicity; RGR of the middle thallus section for As and Cd; ETR_max of the marginal thallus section for Cr; Chl <i>b</i> contents of the marginal thallus section for Cu; RGR of the basal thallus section for Ni. The EC₅₀ values for the inhibition of ETR_max in middle (0.06 mg∙L⁻¹) and Chl <i>b</i> in the marginal thallus sections (0.06 mg∙L⁻¹) were all lower than those of the quality standard for wastewater discharge values of Ag and Cu in Republic of Korea and the US, pointing to the suitability of <i>U. australis</i>-based endpoints for risk assessment.