A system, apparatus and method are described for controlling the gain across one or more amplifier nodes within an optical span. In one embodiment, a fast local amplifier constant gain control loop is provided that maintains a constant gain across an amplifier node for each of the channels within an optical signal. A slow link level gain setting control loop is provided to set and/or adjust the target gain on the amplifier node(s). A gain adjust sequence is performed by the slow link level gain setting control loop to adjust the target gain(s) in response to various events and mechanisms. A "time of flight" protection method is also provided to ensure consistency between the fast local amplifier gain control loop and the slow link level gain setting control loop.