For many years, there has been increasing concern about the effects of the presence of hazardous substances in the environment. The chemical and biological effect (BE) monitoring of these pollutants has proven difficult due to low environmental concentrations, variable bioavailability, and the generalised nature of ecological responses to these substances. The over- or under-expression of key genes has proven to be useful in understanding the molecular mechanisms of the toxicity of contaminants. This study uses a quantitative PCR array to detect the changes in gene expression in flounder livers after exposure to both laboratory- and field-based contaminants. The model contaminants included 17β-estradiol (E2), 3-methylcholanthrene (3-MC), a commercial mixture of polychlorinated biphenyls (PCB, Arochlor), perfluoroctanoic acid (PFOA), and lindane. Multivariate analysis was used to investigate relationships between higher-organisational-level biomarkers, supporting parameters, and genes. A scoring system enabled the visualisation of biological effect responses and contaminants in field samples. Although gene expression was useful for inferring the pathways of toxicity in this organism, we recommend that this array be used in combination with existing and recommended higher-level biomarkers and should not be used as a replacement for traditional biomarkers currently used in monitoring.