Experiencing high cognitive load during complex and demanding tasks results in performance reduction, stress, and errors. However, these could be prevented by a system capable of constantly monitoring users’ cognitive load fluctuations and adjusting its interactions accordingly. Physiological data and behaviors have been found to be suitable measures of cognitive load and are now available in many consumer devices. An advantage of these measures over subjective and performance-based methods is that they are captured in real time and implicitly while the user interacts with the system, which makes them suitable for real-world applications. On the other hand, emotion interference can change physiological responses and make accurate cognitive load measurement more challenging. In this work, we have studied six galvanic skin response (GSR) features in detection of four cognitive load levels with the interference of emotions. The data was derived from two arithmetic experiments and emotions were induced by displaying pleasant and unpleasant pictures in the background. Two types of classifiers were applied to detect cognitive load levels. Results from both studies indicate that the features explored can detect four and two cognitive load levels with high accuracy even under emotional changes. More specifically, rise duration and accumulative GSR are the common best features in all situations, having the highest accuracy especially in the presence of emotions.