A magnetron sputtering system includes a substrate mounted within a vacuum chamber. A plurality of cathode assemblies includes a first set of cathode assemblies and a second set of cathode assemblies, and is configured for reactive sputtering. Each cathode assembly includes a target comprising sputterable material and has an at least partially exposed planar sputtering surface. A target support is configured to support the target in the vacuum chamber and rotate the target relative to the vacuum chamber about a target axis. A magnetic field source includes a magnet array. A cathode assemblies controller assembly is operative to actuate the first set of cathode assemblies without actuating the second set of cathode assemblies, and to actuate the second set of cathode assemblies without actuating the first set of cathode assemblies.