With 6% of Europe's freshwater resources, Switzerland is often considered the ‘water tower of Europe’. Over 8 millions residents rely on more than 57’600 farms to provide meat, milk, or eggs, with 1.58 million cattle, 1.58 million swine or 9.39 million poultry. Livestock farming produce the manure, which is a mixture of urine, faeces and infrastructure washing water. Manure is stockpiled in over 100’000 pits in Switzerland (total capacity of 18 million m3), and then used as fertilizer. When manure enters aquatic environment, such pollution could be responsible of major health risks, contaminating drinkable water sources, or ecological disasters with the death of biota, including fishes. This kind of accident occurs frequently, and authors are in many cases not found by environmental law enforcement. This study aimed at exploring the possibilities of chemical markers to differentiate manures, with the purpose of estimating whether it would be possible to perform source inference in manure pollution cases in a chemical profiling approach. An exploratory market research was first conducted to understand practices of farming chemicals use, including antibiotics and detergents, in order to select potential chemical markers. Manure samples were analysed using ASE-SPE-UPLC-MS/MS (Accelerated Solvent Extraction – Solid Phase Extration – Ultra Performance Liquid Chromatography - tandem Mass Spectrometry) to detect 17 selected chemical markers with Multiple Reaction Monitoring mode: 11 antibiotics (benzylpenicillin, cloxacillin, colistin, danofloxacin, enrofloxacin, neomycin, sufadoxin, sulfaguanidin, sulfamethoxazol, tetracycline and trimetroprim), 1 vermifuge (flubadenzol), 2 local anesthetics (lidocaine and procain), 1 detergent (dodecylbenzenesulfonic acid) and 2 manure/faecal chemical markers (skatole and indole). Analysis in scan mode, extraction of several m/z and statistical testing (PCA and hierarchical cluster analysis) permitted to differentiate manure from cattle and pig farms, and some markers may also be useful to identify a farm among others. Finally, analysis of few specimens collected during pollution events showed that some chemical markers can be found in the water. The results of this study suggest that the applied methodology could allow to identify some types of pollution (including faecal pollution such as manure or wastewater treatment plant malfunctioning), and may help to achieve source inference in environmental fraud cases.