A control system for an engine includes an air calculation module that determines, based on a plurality of first coolant temperatures sensed during a period of engine operation, a first cumulative mass of intake air combusted by the engine during the period that corresponds to an estimated amount of heat dissipated by a cooling system of the engine during the period, and that determines, based on the first cumulative mass, a second cumulative mass of intake air of the engine that is required to raise a temperature of the engine from an initial temperature at a start of the period to a target temperature. The control system further includes a control module that selectively adjusts one of a diagnostic condition and an operating condition of the engine based on the second cumulative mass. A related method for controlling an engine is also provided.