An indirect bonding apparatus for orthodontic bonding procedures includes a tray having inner wall sections defining a channel for receiving the patient's dental arch. A number of orthodontic appliances are detachably connected to the tray along the channel, and each appliance includes a base for bonding the appliance to the tooth. The wall sections include at least one groove extending along the base of at least one appliance in order to provide a space between the wall sections and the patient's tooth structure when the tray is received on the patient's dental arch. The space hinders the flow of oral fluids such as saliva in directions toward the base in order to help ensure that the fluids do not adversely affect the strength of the resulting adhesive bond between the appliance and the tooth.