Our work focused on biocides used in building materials and their transfer to the aquatic environment. This dataset presents the biocide concentrations measured in the dissolved and particulate fractions of different types of urban waters (rain, stormwater, treated and untreated wastewater, combined sewer overflow, surface water) in the Paris conurbation. Data were acquired within the framework of Claudia Paijens' PhD (2019) and with the financial support of the LCPP, the Leesu and the OPUR program. Based on biocide emissions, exposure of the aquatic organisms, ecotoxicity and analytical feasibility, eighteen biocides frequently used in building materials were selected to be monitored in urban waters: diuron, isoproturon, methylisothiazolinone (MIT), chloromethylisothiazolinone (CMIT), benzisothiazolinone (BIT), octylisothiazolinone (OIT), dichloro-octylisothiazolinone (DCOIT), dimethyldidecyl ammonium chloride, benzalkonium chlorides (C12-C16), terbutryn, cybutryn, terbuthylazine, carbendazim, iodopropynyl butylcarbamate (IPBC), thiabendazole, tebuconazole and mecoprop. A multi-residue method was used for the analysis of these biocides in both the dissolved and particulate fractions (filtration through 0.7 µm glass fiber filters) of water samples by liquid chromatography coupled to tandem mass spectrometry. For some compounds, this monitoring led to a unique database, in particular in France. Our results highlighted the ubiquity of the eighteen-targeted biocides in all the urban environment, especially concerning benzalkonium compounds, which were measured at the highest concentrations (in the µg/L range in WWTP influents, WWTP effluents and CSOs, and in the range of 100 ng/L in surface waters for benzalkonium C12). Concentrations significantly higher than 100 ng/L were also measured for MIT and BIT in wastewater. In CSOs, diuron, MIT, carbendazim and mecoprop were quantified at around 100 ng/L. The surface water concentrations were compared to predicted no effect concentrations (PNEC) and pointed out a possible high risk for aquatic ecosystems, more specifically for diuron, carbendazim, DCOIT and benzalkoniums.