Traditional environmental monitoring techniques are well suited to resolving acute exposure effects but lack resolution in determining subtle shifts in ecosystem functions resulting from chronic exposure(s) and multiple stressor contaminants. Ecosurveillance with sensitive omics-based technologies could bridge this gap. The use of omics-based surveillance techniques (particularly metabolomics) for environmental science has grown substantially in the last twenty to thirty years. To date, most omics-based environmental studies have focused on previously degraded environments, identifying key metabolic differences resulting from anthropogenic perturbations. The question many may ask is that why, if environmental metabolomics has so many benefits, it is not used for official environmental testing or policy; why is it not used by industry for environmental testing of new chemicals or products? One would be hard pushed to find an environmental consultant, regulator or policy manager who had heard of metabolomics, let alone who would advocate for its use. What is holding the field back? Here, we present some of the salient environmental metabolomics research applied with CSIROs ecosurveillance efforts. Further, scientists are moving away from individual ‘omic approaches towards a more holistic, systems-based approach for environmental assessment that links genes-proteins-lipids-metabolites. Such a microbial framework would be relevant to ecological investigations measuring the impact of a range of factors, such as climate change, contaminants, disease, food restriction, infection, parasite load, and biogeochemical cycles.