A center pivot irrigation system adapted for variable depth application of water under the corner sprinkler arm. The system includes a pivot sprinkler arm with a first set of nozzles, and a first set of control valves each provided on the pivot sprinkler arm upstream of a nozzle. The irrigation system includes a corner sprinkler arm pivotally coupled to an end of the pivot sprinkler arm, and the corner sprinkler arm includes a second set of spaced apart nozzles and a second set of control valves. The irrigation system includes a controller transmitting control signals to the first and second sets of control valves to open and close in a pattern that includes a valve pulsing pattern for the corner sprinkler arm, whereby input water is applied at a variable rate under the corner sprinkler arm to apply different depths to various user-defined zones.