There are numerous studies on the effects of ocean turbulence on wireless optical communications and on satellite–ground quantum key distribution (QKD); however, there are few studies on the impact of near sea-surface turbulence on ship-based QKD performance. This study investigates the influence of sea-surface atmospheric turbulence on laser beam propagation, atmospheric scintillation, and aiming error. It focuses on the impact of sea-surface turbulence on the performance of satellite-to-ship QKD and ship-to-ship QKD systems. The results show that strong turbulence severely degrades QKD system performance; horizontal transmission distances change from 32 km (weak turbulence) to 3 km (strong turbulence) in ship-to-ship QKD.