In this study, a combination of target and untargeted analytical and chemometric approaches are proposed to assess the metabolic changes of the freshwater flea Daphnia magna produced by the exposure to the environmental endocrine disruptor, bisphenol A. The extraction and analytical procedures were optimized for 23 representative metabolites using different number of daphnids and two different extraction set ups. Control and bisphenol A exposed D. magna extracted samples were then analyzed by liquid chromatography coupled to Orbitrap high resolution mass spectrometry (LC-Orbitrap MS). The targeted analysis of the selected metabolites in control and bisphenol A exposed Daphnia magna samples was first used to assess the analytical protocol and its quantitative performance. In a second stage, an untargeted approach was developed for the analysis and identification of a large number of unknown metabolites expressed or inhibited in the exposed samples to bisphenol in comparison to control samples. For this purpose, the recently developed Regions of Interest - Multivariate Curve Resolution (ROIMCR) procedure as well as other chemometric methods as Principal Component Analysis (PCA) were applied to the data sets gathered by the proposed targeted and untargeted analytical approaches. Results are interpreted in terms of the effects produced by bisphenol A in the metabolism of Daphnia magna and on the discovery of possible biomarkers of exposure.