This dataset includes information collected before and after a 2023 copper treatment was implemented by the State of Idaho to eradicate invasive quagga mussels in the Snake River, Idaho. Water, sediment, periphyton, and macroinvertebrates were sampled at Snake River sites upstream, within, and downstream of the copper treatment reach in order to evaluate the fate and transport of the copper, toxicity to aquatic life, and shifts to benthic community composition. Water samples were analyzed for total and dissolved copper and other parameters of interest to toxicity calculations (such as organic carbon, major metals, anions, and alkalinity). Sediment samples were analyzed for copper, inorganic and organic carbon, and grain size distribution. Periphyton samples were analyzed for biomass, chlorophyll a, and pheophytin a. Macroinvertebrate samples were analyzed for species taxonomy, life stage, and abundance. Population metrics were compiled from the full sample taxonomy including dominance measures, community composition, Karr benthic index of biotic integrity (BIBI) Metrics, functional group composition, stressor identification indices, richness measures, abundance measures, and diversity/evenness measures.