This data collection consists of water quality measurements, nutrient data and measured copper concentrations associated with experiments that derived site-specific guidline values (GVs) for tropical seawater microbiomes by integrating 16S rRNA gene amplicon sequencing with quantitative microbiome profiling and concentration-response modelling. Seawater was collected during high tide at three target sites adjacent to the Burdekin region of the Great Barrier Reef, representing varying disturbance histories: (1) Davies Reef, a high ecological value (HEV) coral reef reference site (S 18°49.826’ E 147°38.177’) situated 50 km offshore with low levels of human impacts and part of the Marine Protected Area; (2) Magnetic Island, a slightly to moderately disturbed (SD-MD) inshore coral/algal reef site (S 19°09.279’ E 146°52.108’) with some perturbations from shipping traffic, dredging, industry, and agricultural runoff; (3) Townsville Breakwater in close proximity to the Port of Townsville, a highly disturbed (HD) inshore site (S 19°14.629’ E 146°49.989’) with increased influence from shipping traffic, industry, and urban runoff. Seawater from each site was subsequently used in a 48-h copper exposure experiment. Water quality measurements (dissolved oxygen, pH and salinity) and water samples for nutrients (dissolved organic / inorganic carbon and nitrogen) were taken at 0-h and 48-h, following standard AIMS procedures. Representative water samples from the nominal experimental treatments (0, 0.1, 0.3, 1, 3, 10, 30, 60, 100, 300, 1000, 3000, 8000 μg Cu L-1) were sent to Envirolab for dissolved copper quantification. Data was entered into excel.