Enrofloxacin is a fluoroquinolone antimicrobial agent used in freshwater rainbow trout against the main pathogenic bacteria Aeromonas salmonicida, Yersinia ruckeri and Flavobacterium psychrophilum. However, the current “standard” dose (10 mg/kg/day for 10 days) was based only on some old, rather limited experimental data, and needed to be re-assessed. Thus, a pharmacokinetic-pharmacodynamic (PKPD) approach was used by combining a population PK model with new epidemiological data (Minimum Inhibitory Concentrations (MIC)) of the three bacterial species to determine optimal enrofloxacin doses in rainbow trout. Ninety-six rainbow trout (half diploid, half triploid) were randomly assigned to four different groups and received oral (gavage) and then intravenous administration of enrofloxacin at four different doses (range 5–60 mg/kg). Individual blood samples were taken to develop a population PK model. Enrofloxacin should be considered as a long-acting drug in trout due to the observed long plasma half-life (>100 h), which is therefore inadequate with the “standard” dosage based on daily oral administrations. Moreover, the fish ploidy had an impact on the PK of enrofloxacin with a longer persistence of enrofloxacin in triploid individuals, which raises the question of the withdrawal period to apply. The absolute bioavailability of oral enrofloxacin was estimated at ~88%. For F. psychrophilum, the provisional epidemiological cut-off value (CONRI), calculated according to the NRI method, was equal to 0.03 μg/mL. For A. salmonicida and Y. ruckeri, however, no clear bimodal distribution of MIC could be observed, and therefore no relevant CONRI could be obtained. According to our model, a single oral dose of ~5 mg/kg should provide sufficient exposure to treat the wild-type population of F. psychrophilum for 4 days, while complying with the PKPD breakpoints. Then, a maintenance dose of ~2.5 mg/kg could possibly be re-administered every 4 days. The absence of a CONRI did not allow to predict an optimal dose for the two other bacteria. As more than 70% of A. salmonicida isolates in our data set have an enrofloxacin MIC ≥0.25 μg/mL, it seems that enrofloxacin should not be recommended against this bacterium. The PKPD approach allowed us to refine the dosing regimens in rainbow trout, for a more sustainable approach. These new dosing regimens have yet to be clinically confirmed.