The presence of anti-microbial-resistant bacteria in the aquatic environment remains a matter of concern for environmental, animal and human health risks. Many published data have reported increased anti-microbial resistance among the aquatic microbiota from fish farm environments which often coincides with the use of anti-microbial agents. It can be assumed that the selection of anti-microbial-resistant bacteria first occurs in the fish farms themselves, at locations where anti-microbial concentrations are active. As anti-microbial agents are frequently administered through feed pellets, faecal matter excreted could favour conditions for such selection. In this study, OA (oxolinic acid) concentrations and OA resistance of Aeromonads were surveyed in output water and in faecal matter from OA medicated (test) and non-medicated (control) fish tanks during and after an OA oral treatment. Because of the low counts of Aeromonads in the output water, it was not possible to obtain reliable data on the proportion of anti-microbial resistance in this compartment. On the other hand, a time-limited effect on the abundance of Aeromonads isolated from faecal matter was only observed in test tanks. In these tanks, high proportion (80–100%) of OA-resistant Aeromonads was present in deposited faecal matter until at least one week after the end of the anti-microbial treatment. At that time OA was no longer detected within the faecal matter, after having reached concentrations between 100 and 190 μg/g during the treatment. We discuss how the leaching of OA from faecal pellets, from the intestine to their deposit, may favour the selection of OA-resistant Aeromonads. Further investigations in real conditions on microbiota associated with faecal matter in transit through the fish farm system are required. Particular attention should be paid to the wastes collected by the filter treatments of fish farm effluents.