Offshore pipelines are often buried in the seabed by ploughing a trench, placing the pipe at the base, and then backfilling. The ploughing operation is critical in terms of cost and project time, with increased risk due to uncertain soil conditions or geohazards. One problem that can be encountered is the presence of sand waves or megaripples on the seabed surface. This may affect the progress of the plough, prevent the plough from generating a level trench or modify the size of the spoil heaps for backfilling. These aspects have been investigated by conducting a series of small-scale model tests in the laboratory. These have revealed information about the plough kinematics and the resulting trench conditions when ploughing in sand waves with different wavelengths and amplitudes. It is shown that it may be possible to plough through regions of sand waves and estimate likely plough performance by knowing the sand wavelength and amplitude relative to the plough size.