Understanding the rapid responses of marine microbiomes to environmental disturbances is of paramount importance for the early assessment of the health of coral reef ecosystems. Yet, global management guidelines aimed at protecting aquatic life from environmental pollution remain exclusively defined for organisms at higher trophic levels. In this study, 16S rRNA gene amplicon sequencing coupled with propidium monoazide for cell-viability assessment was applied as a sensitive tool to determine community-level changes in a seawater microbial community under chronic copper (Cu) exposure. Bayesian model averaging was used to establish concentration-response relationships to evaluate the adverse effects of copper on microbial diversity and composition similarities, for the purpose of estimating No Significant Effect Concentration (NSEC) values. The results demonstrated that microbial diversity and community composition were first affected at concentrations of 0.50 and 1.31 µg Cu L-1 (NSEC), respectively, indicating that low concentrations of copper can impair marine microbiomes. Hazard Concentration (HC) values were estimated for copper below which 99, 95, 90, and 80% of marine microbial taxonomic groups may be protected, by generating an Indicator Taxa Distribution from taxon-specific change points identified using Threshold Indicator Taxa Analysis across the copper gradient. The HC5 guideline value of 0.37 µg Cu L-1 derived for marine microbial communities was lower than the current Australian water quality guideline values based on eukaryotic communities, suggesting that marine microbial communities may not be sufficiently protected from copper pollution. The new approaches employed here provide opportunities for quantitatively assessing the effects of contaminants on microbial communities towards the inclusion of prokaryotes in future water quality guidelines.