A system according to the principles of the present disclosure includes a temperature estimation module and a coolant flow control module. The temperature estimation module can determine an estimate of a heater core air out temperature of a vehicle based upon a heater core inlet coolant temperature, a heater core outlet coolant temperature, an estimated volumetric air flowrate, and an estimated volumetric coolant flowrate. The coolant flow control module can control a rate at which coolant flows to a heater core of the vehicle by adjusting a position of a coolant control valve of the vehicle or an output of a coolant pump of the vehicle. The coolant flow control module can control the coolant flowrate to decrease a difference between a target heater core air out temperature and the estimated heater core air out temperature.