The present invention provides a modular controller that connects to irrigation modules with varying station terminals and a standard footprint size. Additionally, the modular controller includes surge protection options, wireless communication with PDA's and other external devices, no required position for each controller module to be connected, immediate display of station modules on the LCD display, retention of a water program if module is removed, communications module for flow monitoring, a modular transformer, rain sensor receiver within the housing, an improved 9-volt batter holder, and other aspects described in the present application.