A condensate pump for an HVAC system includes a reservoir for collecting condensate water, a pump motor connected to an impeller pump for pumping the condensate water out of the reservoir, and a floatless pump control module. The floatless pump's microcontroller detects the water level in the reservoir and, based on the water level in the reservoir, controls the operation of the pump motor, and if necessary, sounds an alarm and shuts down the HVAC system. The floatless pump microcontroller may employ an ultrasonic transducer or capacitance sensors to detect the level of condensate water in the reservoir. The microcontroller implements a variable water lift feature to pump the water using the lowest possible speed for the pump. The microcontroller implements a self-cleaning feature to pump stagnant water out of the reservoir and to pulse water in the drain line and the agitation of the water in the reservoir. The microcontroller implements an anti-clog feature to clear a clogged drain line when an overflow condition is detected.