The increase in contamination of aquatic environments is concerning as exposure of aquatic organisms such as fish to metals may be lethal. However, studies exploring the molecular changes in fish caused by environmentally realistic concentrations of metals, such as copper (Cu) is limited. Fish in the earlier life stages are even more susceptible to metal-stress than adults, and therefore, this study uses the embryos of the model organism zebrafish (Danio rerio) to investigate changes to the proteome and amino acid (AA) composition of fish exposed to Cu. Wild-type embryos at 24h post-fertilisation (hpf) were exposed to varying concentrations of Cu (2 µg L-1 to 120 µg L-1) for 96h and the number of healthy larvae were determined as larvae that had hatched and not displayed loss of equilibrium (LOE). The effect concentrations which Cu caused a 10% (EC10) or 50% (EC50) decrease in healthy larvae were calculated as 3.7 µg L-1 and 10.9 µg L-1, respectively. Embryos exposed to EC10 and EC50 of Cu exhibited more differentially expressed proteins (DEP) after 48h than 96h, suggesting the acclimatation of some larvae by 96h. Copper exposure caused an increase in the AAs (Valine, Proline and Alanine), as well as the differential expression of proteins involved in combatting oxidative stress and in energy production. Gene ontology and protein-protein interaction networks of the DEP in zebrafish exposed to Cu for 48h showed that DEP were largely associated with visual phototransduction and neural signal transduction. The use of x-ray fluorescence microscopy (XFM) showed an accumulation of Cu and redistribution of Zn to retinal tissue. Together these results may explain the LOE exhibited by some fish at environmentally realistic Cu concentrations. This study shows that the use of proteomics and AA analysis can be used to identify key affected pathways and potential biomarkers for environmental monitoring.