Monitoring benzenesulfonates (BS) and naphthalenesulfonates (NS) took place in five municipal sewage treatment plants (STP). A previously optimized method based on solid phase extraction with polymeric cartridges followed by ion-pair liquid chromatography-electrospray-mass spectrometry (SPE-IPC-ESI-MS) was used. This work confirmed the little or no effect of primary settlement on total organic carbon (TOC) and monosulfonated compounds removal, whereas the main reduction is obtained at the biological stage. However, the most polar compounds, such as naphthalenedisulfonates (NDS), were not effectively removed using the biological treatment. An aromatic sulfonated compound is suggested to be used as a tracer of the origin of industrial pollutants discharged into STPs. A bioluminescence inhibition test, Microtox assay, allowed toxicity determination of the most relevant aromatic sulfonated compounds detected and toxicity comparison between primary and secondary effluents.