Although copper (Cu) is an essential micronutrient for all organisms, in excess, waterborne Cu poses a significant threat to fish from the cellular to population level. We examined the physiological and gene expression endpoints that chronic waterborne Cu exposure (21 d) imposes on soft-water acclimated zebrafish at two environmentally relevant concentrations: 8 µg/L (moderate) and 15 µg/L (high). Using a 16,730 65-mer oligonucleotide customized zebrafish microarray chip related to metal metabolism and toxicity to assess the transcriptomic response, we found that 573 genes in the liver responded significantly to copper exposure. These clustered into 3 distinct patterns of expression. There was distinct up- regulation of a majority of these genes under moderate Cu exposure, and a significant down-regulation under high Cu exposure. Microarray results were validated by qPCR of 8 genes; 2 genes, metallothionein 2 (mt2) and Na⁺K⁺ATPase 1a1 (atp1a1), displayed increased expression under both Cu exposures, indicative of potential genetic endpoints of Cu toxicity, whereas the remaining 6 genes demonstrated opposing effects at each Cu exposure. Na⁺K⁺ATPase enzyme activity decreased during Cu exposure, which may be linked to Cu's competitive effects with Na⁺. Whole-body cortisol levels were significantly increased in Cu-exposed fish, which prompted an analysis of the promoter region of all significantly regulated genes for glucocorticoid (GRE) and metal (MRE) response elements to dissociate metal- and stress-specific gene responses. Of the genes significantly regulated, 30% contained only a GRE sequence, whereas 2.5% contained only a consensus MRE. We conclude that the indirect effects of Cu exposure regulate gene expression to a much greater degree than the direct effects.