Abstract This paper investigates climate change signals of Southern Hemisphere (SH) moisture flux simulated by three members of one CMIP3 coupled atmosphere–ocean general circulation model (AOGCM) and a multimodel ensemble of CMIP5 simulations. Generally, flux changes are dominated by increased atmospheric moisture due to temperature increase in the future climate projections. An approach is presented to distinguish between thermodynamical and dynamical influences on moisture flux. Furthermore, a physical interpretation of the transport changes due to dynamics is investigated by decomposing atmospheric waves into different length scales and temporal variations. Signals of moisture flux are compared with fluctuations of geopotential height fields as well as climate signals of extratropical cyclones. Moisture flux variability in the synoptic length scale with temporal variations shorter than 8 days can be assigned to the SH storm track. Climate change signals of these atmospheric waves show a distinctive poleward shift. This can be attributed to the climate change signal of extratropical cyclones. Furthermore, the climate change signal of atmospheric waves can be better understood if strong cyclones that intensify especially on the Eastern Hemisphere are taken into account. Antarctic net precipitation is calculated by means of the vertically integrated moisture flux. Future projections show increasing signals of net precipitation, whereas the dynamical part of net precipitation decreases. This can be understood by means of the low-variability component of synoptic-scale waves, which show a decreasing signal, especially off the coast of West Antarctica. This is shown to be due to changing variability of the Amundsen–Bellingshausen Seas low.