The influence of a neutral atmospheric boundary layer on a one-way coupled dynamic interface simulation is evaluated. The effort is performed within the context of time-accurate large-eddy simulations of Simple Frigate Shape 2, which is immersed into a turbulence-resolving atmospheric inflow that emulates the dynamics of a realistic atmospheric boundary layer. Several baseline cases are used to represent a traditional approach of modeling the incoming wind as a constant, uniform inflow. When comparing the atmospheric boundary layer-resolving to the baseline simulations, it is observed that the velocities in a ship airwake are considerably different when formed from an atmospheric boundary layer. The unsteady computational fluid dynamics solution is then saved as a database and used as external disturbances for flight dynamics analysis. Such an approach is common in piloted flight simulation. The pilot workload is evaluated using a helicopter approach scenario and multiple hover locations. Such cases are evaluated, and it is found that the large scales present in the atmospheric boundary layer notably disturb the helicopter. The disturbances result in increased controls input and aircraft movement. Frequency-domain analysis of the increased stick movement suggest that the atmospheric boundary layer impacts the 0.1–2 Hz stick controls, which comprise the frequency range known to affect pilot workload.