Antimicrobial resistance (AMR) arises mostly because of the use and abuse of antibiotics in both the human and veterinary sectors. Furthermore, antibiotic residues can be discharged into the environment, promoting the spread of AMR as well as becoming a potential ecotoxicological risk. Aquaculture is one such source of environmental pollution. In the present work, we evaluated the correlation between antibiotic consumption in 11 selected aquafarms located along the Nera River, and the detection of their residues in surface water and sediment samples gathered monthly from the same stream. Antibiotic consumption was calculated using the ESVAC defined daily doses for animals (DDDvet) method, and a chemical analysis was conducted using a multiclass method. Therefore, the ecological risk of antibiotics being detected in surface waters was established based on the risk quotient (RQ). A strong positive correlation was identified between the concentrations detected in surface waters and the consumption of flumequine (r = 72%, p-value = 0.0085) and florfenicol (r = 83%, p-value = 0.0008). The RQ, however, was low for all the detected antibiotics in surface waters. Therefore, we proved that the antibiotics used in aquaculture can reach the near aquatic environment, but, in this work, they did not represent a toxicological risk to the surrounding ecosystem.