The ship air-wake over the landing deck of a NATO-Generic Destroyer model is investigated experimentally to better understand the effects of the Atmospheric Boundary Layer (ABL) on the flow. Two methods of creating thick ABLs are employed: i. using a series of tripping devices in a typical wind tunnel; ii. by performing the test on a water surface in a wind-wave facility. In comparison with a smooth-wall (unstimulated) boundary layer, the wake of the ship is substantially modified for both ABL cases. The ABL increases the overall fluctuation levels over the landing deck, highlighting the importance of including an ABL in simulations or experiments. Specifically, we show that the streamwise fluctuation on the landing deck increases linearly with both the background turbulence and the reference mean velocity; a simple relationship is provided. We consider the sensitivities of the wake to ABL scaling (relative to ship height), noting that a thicker ABL will generally lead to lower fluctuation levels in the wake over the landing deck (in the absence of free stream turbulence intensity).