Metal contamination of aquatic environments remains a major concern due to their persistence. The water flea Daphnia magna is an important model species for metal toxicity studies and water quality assessment. However, most research has focused on physiological endpoints such as mortality, growth, and reproduction in laboratory settings, as well as neglected toxicogenomic responses. Copper (Cu) and zinc (Zn) are essential trace elements that play crucial roles in many biological processes, including iron metabolism, connective tissue formation, neurotransmitter synthesis, DNA synthesis, and immune function. Excess amounts of these metals result in deviations from homeostasis and may induce toxic responses. In this study, we analyzed Daphnia magna transcriptomic responses to IC5 levels of Cu (120 µg/L) and Zn (300 µg/L) in environmental water obtained from a pristine lake with adjusted water hardness (150 mg/L CaCO3). The study was carried out to gain insights into the Cu and Zn regulated stress response mechanisms in Daphnia magna at transcriptome level. A total of 2,688 and 3,080 genes were found to be differentially expressed (DEG) between the control and Cu and the control and Zn, respectively. There were 1,793 differentially expressed genes in common for both Cu and Zn, whereas the number of unique DEGs for Cu and Zn were 895 and 1,287, respectively. Gene ontology and KEGG pathways enrichment were carried out to identify the molecular functions and biological processes affected by metal exposures. In addition to well-known biomarkers, novel targets for metal toxicity screening at the genomic level were identified.