Livestock manure containing antimicrobials becomes a possible source of these compounds to surface and ground waters when applied to cropland as a nutrient source. The potential for transport of the veterinary antimicrobial lincomycin to surface waters via surface runoff and to leach to ground water was assessed by monitoring manure-amended soil, simulated rainfall runoff, snowmelt runoff, and ground water over a 2-yr period in Saskatchewan, Canada, after fall application of liquid swine manure to cropland. Liquid chromatography tandem mass spectrometry was used to quantify lincomycin in all matrix extracts. Initial concentrations in soil (46.3-117 mug kg(-1)) were not significantly different (p > 0.05) for manure application rates ranging from 60,000 to 95,000 L ha(-1) and had decreased to nondetectable levels by mid-summer the following year. After fall manure application, lincomycin was present in all simulated rainfall runoff (0.07-2.7 mug L(-1)) and all snowmelt runoff (0.038-3.2 mug L(-1)) samples. Concentrations in snowmelt runoff were not significantly different from those in simulated rainfall runoff the previous fall. On average, lincomycin concentrations in ephemeral wetlands dissipated by 50% after 31 d. Concentrations of lincomycin in ground water were generally <0.005 mug L(-1). This study demonstrates that the management practice of using livestock manure from confined animal feeding operations as a plant nutrient source on cropland may result in antimicrobial transport to surface and ground waters.