The system of the present invention provides energy saving control for a water heater via an intelligent thermostat. This intelligent thermostat provides programmatic control over the HVAC system as is conventional, and provides coordinated control over the water heater temperature set point. This control over the water heater is accomplished via a communications network between the intelligent thermostat and the water heater. In one embodiment the communications are wireless, although wired and network bus communications may also be utilized. Enhanced and coordinated control is also provided so that different operational temperature cycles can be provided to coordinate with the intelligent thermostat's programmatic control of the HVAC system. Separate programmatic control of the water heater is also provided whereby different operational temperature modes may be commanded, e.g. Wake, Sleep, and Demand modes of operation.