We systematically assess the efficiency of chemical cleaning and report a simple but elegant approach to control scaling during membrane distillation (MD) of brine from reverse osmosis (RO) treatment of coal seam gas (CSG) produced water. Results reported here show that increased feed water salinity and the permeation of CO2 from the feed solution resulted in only a small and gradual decrease in water flux. On the other hand, the precipitation of sparingly soluble salts on the membrane at high water recovery (>70%) led to a significant flux decline. Among the three chemical cleaning agents investigated, a reverse osmosis scale cleaning agent (denoted as MC3) was the most effective at restoring the water flux; however, MC3 cleaning was not able to completely remove scale deposits from the membrane and restore its surface hydrophobicity to the original value because of the complexation of scalants with CSG RO brine. The remaining scalants (i.e., silicates) reduced the membrane surface hydrophobicity and could possibly enhance concentration polarisation and act as seeding for further scale formation. Thus, a gradual decrease in MD performance with respect to both water flux and salt leakage was observed after each MC3 cleaning cycle. It was noted that the chemical cleaning agents themselves did not alter the hydrophobicity of the membrane; thus, the gradual decline in MD performance was attributed to the remaining scale deposits on the membrane after each cleaning cycle. Results reported here highlight the need to prevent membrane scaling and only use chemical cleaning as the last resort during MD treatment of CSG RO brine. Moreover, membrane scaling could be prevented by reducing concentration polarisation via limiting feed temperature and thus water flux. MD treatment of CSG RO brine with up to 80% water recovery without any observable membrane scaling was achieved at the feed temperature and the water flux of 35°C and 10L/m2h, respectively.