Heat exchangers require periodic maintenance. Offline cleaning scheduled shutdowns are usually needed to restore the exchanger effectiveness, drastically reduced when fouling accumulation occurs. An online real-time alternative for monitoring the effectiveness of exchanger (during a period of eleven months of continuous operation) and an adapted version of the ε-NTU method to calculate its effectiveness are discussed. The experimental difficulties of measuring the mass flow rate and the hot air temperature at the exit of the exchanger is examined. Detailed analysis confirmed that the outlet temperature of the hot fluid could introduce errors of up to 30% in the calculation of the exchanger effectiveness. A skillful treatment of the energy balance is proposed to address the issue. The associated uncertainties are estimated by two independent approaches, the so-called classic method, i.e., the Guide to the Expression of Uncertainty in Measurement and the Monte Carlo method. Both confirmed that measurements of the air outlet temperature accounts for more than 50% of the uncertainty associated with the calculation of the exchanger effectiveness. It is suggested that the conventional method (based on measurements of the outlet air temperature) is not suitable for traditional everyday practices to monitor the effectiveness of the heat exchangers of hydrogenerators.