This paper discusses the utilization of pilots' physiological indications such as electroencephalographic signals, ocular parameters, and pilot performance-based quantitative metrics to estimate cognitive workload. The study aims to derive a non-invasive technique to estimate pilot's cognitive workload and study their correlation with standard physiological parameters. Initially, we conducted a set of user trials using well-established psychometric tests for evaluating the effectiveness of pupil and gaze-based ocular metrics for estimating cognitive workload at different levels of task difficulty and lighting conditions. Later, (...) we conducted user trials with the NALSim flight simulator using a business class Learjet aircraft model. We analyzed participants' ocular parameters, power levels of different EEG frequency bands, and flight parameters for estimating variations in cognitive workload. Results indicate that introduction of secondary task increases pilot's cognitive workload significantly. The beta frequency band of EEG, nearest neighborhood index specifying distribution of gaze fixation, L1 Norm of power spectral density of pupil diameter, and the duty cycle metric indicated variations in cognitive workload. (shrink)