The present report describes a rapid and sensitive ultra high-pressure liquid chromatography (UHPLC) method with UV detection to quantify moxifloxacin in rabbit aqueous humor. After deproteinisation with acetonitrile, gradient separation of moxifloxacin was achieved on a Waters Acquity BEH C18 (50 mm × 2.1 mm, 1.7 μm) column at 50 °C. The mobile phase consisted of 0.1% trifluoroacetic acid in water and acetonitrile at a flow rate of 0.4 ml/min. Detection of moxifloxacin was done at 296 nm. Method was found to be selective, linear ( r = 0.9997), accurate (recovery, 97.30–99.99%) and precise (RSD, ≤1.72%) in the selected concentration range of 10–1000 ng/ml. Detection and quantitation limit of moxifloxacin in aqueous humor were 0.75 and 2.5 ng/ml, respectively. The aqueous humor levels of moxifloxacin after single topical instillation in three formulations, i.e. moxifloxacin solution (Moxi-SOL), anionic nanoparticles (Moxi-ANP) and cationic nanoparticles (Moxi-CNP) were investigated. A fourfold increase in the relative bioavailability was observed with the Moxi-CNP (AUC 0→ t , 3.14 μg h/ml) compared with Moxi-SOL (AUC 0→ t , 0.79 μg h/ml) and Moxi-ANP (AUC 0→ t , 0.72 μg h/ml) formulation. The results indicate that the cationic nanoparticle increases ocular bioavailability of moxifloxacin and prolong its residence time in the eye.