Ecotoxicogenomic approaches to environmental monitoring provide holistic information, offer insight into modes of action, and help to assess the causal agents and potential toxicity of effluents beyond the traditional end points of death and reproduction. Recent investigations of toxicant exposure indicate dose-dependent changes are a key issue in interpreting genomic studies. Additionally, there is interest in developing methods to integrate gene expression studies in environmental monitoring and regulation, and the No Observed Transcriptional Effect Level (NOTEL) has been proposed as a means for screening effluents and unknown chemicals for toxicity. However, computational methods to determine the NOTEL have yet to be established. Therefore, we examined effects on gene expression in Daphnia magna following exposure to Cu, Cd, and Zn over a range of concentrations including a tolerated, a sublethal, and a nearly acutely toxic concentration. Each concentration produced a distinct gene expression profile. We observed differential expression of a very few genes at tolerated concentrations that were distinct from the expression profiles observed at concentrations associated with toxicity. These results suggest that gene expression analysis may offer a strategy for distinguishing toxic and nontoxic concentrations of metals in the environment and provide support for a NOTEL for metal exposure in D. magna. Mechanistic insights could be inferred from the concentration-dependent gene expression profiles including metal specific effects on disparate metabolic processes such as digestion, immune response, development and reproduction, and less specific stress responses at higher concentrations.