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Little is known regarding the impact excessive waterborne metals, like copper (Cu), have on tropical freshwater species. Zebrafish (Dania rerio) only recently became popular as a tool for environmental monitoring, due to their fully sequenced genome. Despite this, little was known regarding the ionoregulatory physiology of zebrafish. I first examined the impact softwater acclimation has on the ionoregulatory capacity of zebrafish, and identified a high degree of phenotypic plasticity associated with changes in both gene and protein expression, which highlighted the need for proper experimental design for studies involving pre-acclimation to softwater. I then examined the acute and chronic effects of waterborne Cu exposure under the influence of both softwater conditions and the addition of protective ions (Na+ & Ca2+) . On an acute timeframe, I found that Na+ provided a greater protective effect than Ca2+ in reducing Cu uptake, which was mimicked during chronic exposure, although the transcriptional effects were not as clear cut. I found that although Na+ and Ca2+ provided protective effects from Cu accumulation, there were still tissue specific and global changes at the transcript level, as determined by microarray analysis. Furthemore, this set of experiments identified the metal- and stress- induced transcriptional effects due to Cu exposure, which is key to identifying gene endpoints of chronic Cu exposure. A final experiment went further and looked at the effects of mixed metal contamination, examining chronic waterborne Cu exposure with interactive effects of elevated dietary Fe on gene expression and tissue metal accumulation. Not only did this experiment highlight that gene expression is not necessarily reflected in protein abundance/activity, but also demonstrated that high dietary Fe can significantly alter the transcriptional expression pattern of Cu transporters in the gill, liver, and gastrointestinal tract. This thesis has made significant steps in identifying viable gene endpoints of Cu toxicity. Thesis Doctor of Philosophy (PhD)