Metabolomics, the global profiling of metabolite composition, is a powerful technique that can be applied to answer a diverse set of research questions concerning effects of toxicants on organisms. It has recently emerged as a tool to understand complex environmental perturbations in biological systems, especially at sub-lethal concentrations. Organisms can be affected by different stressors such as xenobiotics or increase in concentration of natural compounds such as nitrogen, phosphorous, and sulfur. Metabolomics has facilitated a better understanding of the effects of these perturbations on organisms such as plants, animals, and humans providing phenotypic and biological information in a high throughput manner. In this review, we will discuss recent applications of metabolomics to study the ecological effects of different environmental perturbations, including nanoparticles, pharmaceuticals and personal care products, pesticides, as well as the changes in natural compounds found in the environment with a focus on plant systems.