Nitrilotriacetic acid (NTA) and ethylenediaminetetraacetic acid (EDTA), as widely used chelating agents, have created many environmental issues and raised much attention regarding their environmental occurrence. However, the determination of NTA and EDTA in samples of complex solution chemistry remains challenging. Here, we proposed a simple and sensitive method based on liquid chromatography tandem mass spectrometry (LC-MS/MS) to determine NTA and EDTA from aqueous samples without an enrichment step. During the analysis, H+-cation exchange was used to efficiently eliminate interference from metal ions. The intensity of NTA and EDTA with trimethylsilyldiazomethane methylation could be improved hundreds of times that of the virgin samples. To maximize sensitivity, the sample pretreatment methods, the derivatization procedures and the LC-MS/MS conditions were systematically optimized. The validated method showed low limits of quantification (0.4 μg/L for NTA and 1.5 μg/L for EDTA), a wide linear response (up to several mg/L, R2 > 0.998), and good intra- and inter-day precision (relative standard deviation ≤ 11%). The reliability of this method was successfully validated by analysis of authentic water samples collected from three WWTPs and one river with satisfactory recoveries (80–117%). It can be proposed as a powerful analytical method of NTA and EDTA in authentic water samples and could potentially be adapted to detect other chelates and polydentate compounds.