Sustainable food systems imply the re-use of biowastes and water. In this paper we characterize 30 top soil improvers of anthropogenic, animal and green waste origin, and 11 irrigation waters from rivers, channels, and civil wastewater treatment plants (cWWTPs) for the presence of antimicrobials. Liquid chromatography coupled to hybrid High Resolution Mass Spectrometry (LC-HRMS/MS) was applied to determine 50 different drugs belonging to the classes of sulfonamides (11), tetracyclines (7), fluoroquinolones (10), macrolides (12), amphenicols (3), pleuromutilins (2), diaminopyrimidines (1), rifamycines (1) and lincosamides (1). Biowastes from cWWTPs and animal manure, slurry and litter revealed the highest loads for sulfonamides, tetracyclines, fluoroquinolones, and macrolides (80, 470, 885, and 4,487 ng/g wet weight, respectively) with nor- and cipro-floxacin as marker of anthropogenic sources. In composts and digestates antimicrobials were almost below the determination limits. Re-used waters for irrigation in open field lettuce production resulted contaminated in the range of 12-221 ng/L for sulfonamides, tetracyclines, and fluoroquinolones, against very few detects in channels and surface waters. Antimicrobials Hazard Index (HI) based on Predicted No Effect Concentration for Antimicrobial Resistance (PNECAMR) was largely >100 in contaminated top soil improvers from urban and animal sources. Accounting for worst-case inputs from top soil improvers and irrigation water and dilution factors of amended soil, fluoroquinolones only showed a HI around 1 in open fields for lettuce production. The origin of top soil improvers plays a pivotal role for safe and sustainable leafy vegetable productions, to abate the risk of AMR onset in food-borne diseases, as well the transfer of AMR elements to human gut flora.