Environmental releases of antibiotics from concentrated animal feeding operations (CAFOs) are of increasing regulatory concern. This study investigates the use and occurrence of antibiotics in dairy CAFOs and their potential transport into first-encountered groundwater. On two dairies we conducted four seasonal sampling campaigns, each across 13 animal production and waste management systems and associated environmental pathways: application to animals, excretion to surfaces, manure collection systems, soils, and shallow groundwater. Concentrations of antibiotics were determined using on line solid phase extraction (OLSPE) and liquid chromatography-tandem mass spectrometry (LC/MS/MS) with electrospray ionization (ESI) for water samples, and accelerated solvent extraction (ASE) LC/MS/MS with ESI for solid samples. A variety of antibiotics were applied at both farms leading to antibiotics excretion of several hundred grams per farm per day. Sulfonamides, tetracyclines, and their epimers/isomers, and lincomycin were most frequently detected. Yet, despite decades of use, antibiotic occurrence appeared constrained to within farm boundaries. The most frequent antibiotic detections were associated with lagoons, hospital pens, and calf hutches. When detected below ground, tetracyclines were mainly found in soils, whereas sulfonamides were found in shallow groundwater reflecting key differences in their physicochemical properties. In manure lagoons, 10 compounds were detected including tetracyclines and trimethoprim. Of these 10, sulfadimethoxine, sulfamethazine, and lincomycin were found in shallow groundwater directly downgradient from the lagoons. Antibiotics were sporadically detected in field surface samples on fields with manure applications, but not in underlying sandy soils. Sulfadimethoxine and sulfamethazine were detected in shallow groundwater near field flood irrigation gates, but at highly attenuated levels.