Emerging contaminants are a heterogeneous group of chemicals that includes daily personal care products and pharmaceuticals (PPCPs), flame retardants, endocrine disrupting chemicals (EDCs) and nanoparticles (NPs) present in environment which are unregulated. In this review are presented the methods of analysis conducted by INCD-ECOIND regarding some classes of emerging contaminants (neonicotinoids compounds, beta-blockers) that are not mentioned in the legislation, in different types of environmental samples (influent and effluent). The paper presents the selective solid phase extraction (SPE) methods for isolating the compounds of interest from aqueous matrices and the main operating parameters of the separation process. Then, the compounds were subjected to liquid phase chromatographic separation with mass spectrometric detection (UHPLC-MS/MS). Thus, the main instrumental operating parameters used for the analytical determination of the emerging contaminants studied are presented. Finally, the methods were applied in the determination of compounds from different categories of water, carrying out studies on the efficiency of elimination of compounds in several municipal wastewater treatment plants (WWTPs).