This dataset has been acquired from road runoff samples collected as part of the Roulepur project (Office Français de la Biodiversité, Agence de l’eau de Seine-Normandie). All samples were extracted by SPE with HLB cartridges at pH 2. Data was acquired with a UPLC-IMS-QTOF (Waters Vion) running Unifi, in HDMSe mode. Samples were injected in a random sequence (see order in samplemetadata.csv file). A list of markers was obtained from Unifi after alignment across all samples, and exported as a markertable.csv file. Each detected marker has m/z, retention time, drift time (ion mobility) values, and intensity values in all samples. Raw data was converted using Proteowizard MSConvert version 3.0.19014-f9d5b8a3b, using zlib compression, combining ion mobility scans, with the CWT peakpicking algorithm (snr=0, peakSpace=0) to transform profile to centroid data, and the zeroSamples option (removeExtra 1-). The chosen output format was .mz5. For file naming explanation, see the readme.txt file.