A fluoroquinolone/glucocorticoid combination for the treatment of bacterial keratitis in the form of mucoadhesive nanoparticle suspensions was developed to prolong the release and improve patient compliance. Gatifloxacin/prednisolone loaded nanoparticles were prepared using Eudragit RS 100 and RL 100 and coated with the bioadhesive polymer, hyaluronic acid. FT-IR and DSC studies revealed no interaction between gatifloxacin and prednisolone. The effects of the drug:polymer ratio (D:P) and the RS/RL ratio were studied. The obtained nanoparticles were distinct and spherical with a solid dense structure. They have average particle size range of 315.2 to 973.65 nm. Increasing the D:P ratio significantly lowered the entrapment efficiency for both drugs (p < 0.05). The nanoparticle suspensions revealed significantly prolonged drug release comparing to the free drugs (p < 0.05) with no burst effect. Increasing the polymer concentration and the Eudragit RS ratio significantly decreased the release efficiency values. Gatifloxacin showed anomalous release (n = 0.4943) from 1:1 D:P ratio nanoparticle suspension and Fickian diffusion mechanism (n < 0.45) from formulas prepared at higher D:P ratios. Gatifloxacin showed better bioavailability and sustained action in aqueous humor and corneal tissue from the nanoparticles compared to the commercial eye drops. The resulting nanoparticle suspension is promising in reducing dose frequency and improving patient compliance.