Ecotoxicogenomics might help solving open questions that cannot be answered by standard ecotoxicity tests currently used in environmental risk assessment. Changes in gene expression are claimed to serve potentially as early warning indicators for environmental effects and as sensitive and specific ecotoxicological end points. Ecotoxicogenomics focus on the lowest rather than the highest levels of biological organization. Our aim was to explore the links between gene expression responses and population level responses, both mechanistically (conceptual framework) and correlatively (Species Sensitivity Distribution). The effects of cadmium on aquatic species were compared for gene level responses (Lowest Observed Effect Concentrations) and individual level responses (median Lethal Concentrations, LC(50), and No Observed Effect Concentrations, NOEC). Responses in gene expression were on average four times above the NOEC and eleven times below the LC(50) values. Currently, use of gene expression changes as early warning indicators of environmental effects is not underpinned due to a lack of data. To confirm the sensitivity claimed by ecotoxicogenomics more testing at low concentrations is needed. From the conceptual framework, we conclude that for a mechanistic gene population link in risk management, research is required that includes at least one meaningful end point at each level of organization.