Honey is a rich source of carbohydrates, while minor compounds such as amino acids and polyphenols contribute to its health-promoting effects. Honey is one of the oldest traditional remedies applied for microbial infections, due to its antibacterial, anti-inflammatory, and antioxidant properties. The aim of this study was to investigate the antibacterial and antibiofilm effects of Hungarian black locust, linden, and sunflower honeys against the most common biofilm-forming respiratory tract pathogens Haemophilus spp., Pseudomonas aeruginosa, and Streptococcus pneumoniae. The unifloral character of all three honey types was confirmed by melissopalynological analysis. The antibacterial activity of each honey sample against each bacterium strain was proven with agar well diffusion assay and thin layer chromatography—direct bioautography. Kinetics and mechanisms of antibacterial action were clarified with time-kill assay and membrane degradation study. The anti-biofilm activity was evidenced using crystal violet assay. In each assay, linden honey was the most effective, followed by sunflower and black locust honey. In addition, each honey sample had greater potential to suppress respiratory tract bacteria, compared to major sugar components. In conclusion, honey in general and linden honey in particular, can have a role in the treatment of respiratory tract infections caused by biofilm-forming bacteria.