Although the atmospheric sciences community has been studying the effects of atmospheric stability and surface roughness on the planetary boundary layer for some time, their effects on wind turbine dynamics have not been well studied. In this study, we performed numerical experiments to explore some of the effects of atmospheric stability and surface roughness on wind turbine dynamics. We used large-eddy simulation to create atmospheric winds and compute the wind turbine flows, and we modeled the wind turbines as revolving and flexible actuator lines coupled to a wind turbine structural and system dynamic model. We examined the structural moments about the wind turbine blade, low-speed shaft, and nacelle; power production; and wake evolution when large 5-MW turbines are subjected to winds generated from low-and high-surface roughness levels representative of offshore and onshore conditions, respectively, and also neutral and unstable atmospheric conditions. In addition, we placed a second turbine 7 rotor diameters downwind of the first one so that we could explore wake effects under these different conditions. The results show that the turbulent structures generated within the atmospheric boundary layer wind simulations cause isolated loading events at least as significant as when a turbine is waked by an upwind turbine. The root-mean-square (RMS) turbine loads are consistently larger when the surface roughness is higher. The RMS blade-root out-of-plane bending moment and low-speed shaft torque are higher when the atmospheric boundary layer is unstable as compared with when it is neutral. However, the RMS yaw moments are either equal or reduced in the unstable case as compared with the neutral case. For a given surface roughness, the ratio of power produced by the downwind turbine relative to that of the upwind turbine is 15-20% higher when the conditions are unstable as compared with neutral. For a given atmospheric stability, this power ratio is 10% higher with the onshore roughness value versus the offshore one. The main conclusion is that various coherent turbulent structures that form under different levels of atmospheric stability and surface roughness have important effects on wind turbine structural response, power production, and wake evolution.