Methods for removing debris and bacteria from tooth and orthopedic surfaces using irrigation solutions are provided. The solution includes disinfectant, surfactant, and organic acid components. Disinfectants such as tetracycline and doxycycline compounds can be used. Suitable surfactants include cocamidopropyl betaine compounds and polyoxypropylene-polyoxyethylene copolymers. The solution is particularly suitable for removing smear layers from tooth surfaces during root canal treatment and other dental procedures such as restoration, reconstruction, and periodontal work. The solutions also can be used to remove smear layers from bone surfaces.