AbstractGroundwater samples may contain thousands of organic pollutants from infiltration of surface water, sewer leakages, and to a minor extent from public water supply network losses. Polar (0 < log D < − 2.0) and very polar substances (log D < − 2.0) have been largely beyond the scope of applied analytical methodologies in environmental monitoring because of challenges related to their extraction from the sample and subsequent chromatographic separation. In this study, we developed an analytical workflow for 96 pollutants covering a broad polarity range, including pharmaceuticals, industrial chemicals, and artificial sweeteners, potentially seeping through the soil in urban areas. The Besos aquifer located at the Northern-eastern edge of the city of Barcelona was chosen as a study area due to the deterioration of the quality of the aquifers over the past years and the proven presence of numerous pollutants. The methodology consisted of vacuum-assisted evaporation (VAE) followed by chromatographic separation of the sample on two columns with orthogonal retention mechanisms, namely, an HSS T3 column (modified C18) and a BEH amide column (HILIC). The analytes were detected by high-resolution mass spectrometry on a Q Exactive Orbitrap system in data-independent acquisition mode. Taking into consideration the retention as well as the peak shape, a Quality Score (QS) was assigned for each analyte to evaluate the quality of each chromatographic peak of each compound. While 67 compounds, including 19 polar and 48 moderately polar, were satisfactorily retained on an HSS T3, 29 compounds, including 14 highly polar, 14 polar, and one moderately polar, were analyzed in the BEH amide column. The optimized methodology was applied for the analysis of 89 out of 96 validated contaminants with satisfactory recoveries in samples collected from seven wells, providing low LODs (0.02 to 0.45 ng L−1) and LOQs (0.06 to 1.34 ng L−1). A number of highly polar and polar compounds not previously reported to occur in GW, including artificial sweeteners, pharmaceuticals, and industrial chemicals, were detected at concentrations as high as few $$\mu$$ μ g L−1.