This is the first study to implement a genomic approach to ascertain both transcriptional and functional end points of chronic Cu toxicity in fish associated with experimentally manipulated water chemistries. Over 21 d, zebrafish acclimated to softwater (Na(+) = 0.06 mM, Ca(2+) = 0.08 mM, Mg(2+) = 0.03 mM) were exposed to the following: soft-water (Ctrl); 12 microg L(-1) Cu (Cu); 3.3 mM Na(+) (Na); 3.3 mM Na(+) + 12 microg L(-1) Cu (Na + Cu); 3.3 mM Ca(2+) (Ca); or 3.3 mM Ca(2+) + 12 microg L(-1) Cu (Ca + Cu). Although effective at reducing Cu load in all tissues, Na(+) in the presence of Cu did not decrease the degree of oxidative damage, particularly in the gill and gut. In contrast, Ca + Cu treatment decreased Cu accumulation in gill, but not liver or gut, with no reduction in oxidative damage. Transcriptional analysis of candidate genes (atp7a, ctr1, ECaC, esr1) showed principally a down regulation of transcripts with the Cu only treatment, while Ca + Cu treatment restored some of the genes to control levels. Conversely, the Na + Cu treatment had a strong, opposing affect when compared to that of Cu alone. Zebrafish Affymetrix GeneChips revealed significantly clustered patterns of expression. Changes in expression induced by Cu appeared to be opposite to the majority of the other treatments. Our data on the preventative or enhancing effects of Na(+) and Ca(2+) both alone and in the presence of Cu, may, in the future, facilitate the incorporation of gene expression end points into a biotic ligand model predicting chronic Cu toxicity in this tropical model species of genomic importance.