One central topic in ergonomics and human-factors research is the assessment of mental workload. Heart rate and heart rate variability are common for registering mental workload. However, a major problem of workload assessment is the dissociation among different workload measures. One potential reason could be the disregard of their inherent timescales and the interrelation between participants' individual differences and timescales. The aim of our study was to determine if different cardiovascular biomarkers exhibit different timescales. We focused on air traffic controller and investigated biomarkers' ability to distinguish between conditions with different load levels connected to prior work experience and different time slots. During an interactive real-time simulation, we varied the load situations with two independent variables: the traffic volume and the occurrence of a priority-flight request. Dependent variables for registering mental workload were the heart rate and heart rate variability from two time slots. Our results show that all cardiovascular biomarkers were sensitive to workload differences with different inherent timescales. The heart rate responded sooner than the heart rate variability features from the frequency domain and it was most indicative during the time slot immediately after the priority-flight request. The heart rate variability parameters from the frequency domain responded with latency and were most indicative during the subsequent time slot. Furthermore, by consideration of biomarkers' inherent timescales, we were able to assess a significant effect of work experience on heart rate and mid/high frequency-band ratio of the heart rate variability. Results indicated that different cardiovascular biomarkers reveal different inherent timescales.