Veterinary antimicrobials can spread via manure onto agricultural fields, representing an emission of these products or their active metabolites into the environment. This causes concerns regarding the role of antimicrobial residues in the development, selection and spread of resistance. Aiming to approach this issue quantitatively, first a literature review was performed on the bioavailability and extent of in vivo biotransformation of twelve antimicrobials commonly used in pigs orally, and on the level of their persistence in manure. This information was then used in a model estimating the level of each of these administered antimicrobials that is present in manure at the end of common storage durations in pits and, thus, readily applied onto soil. From the studied antimicrobials, the highest level of residues in stored manure was estimated for doxycycline (55% of the initial amount of doxycycline administered orally to pigs after six months of manure storage), as a combining result of its high use in pigs, low bioavailability and high stability in manure. Other antimicrobials (e.g. amoxicillin) are readily degraded and therefore pose less threat. The results of this study highlight the importance of rational antimicrobial use and of further research on pharmacokinetics of antimicrobials and their degraded products in different environmental compartments, to efficiently control the spread of residues and/or resistance genes from manure to these matrices.