Seawater desalination has become an essential part of the drinking water supply of many arid countries in the world - including Cyprus and the wider Mediterranean - Middle Eastern region. In this study, the microinvertebrate fauna near the outfall sites of 2 seawater desalination plants, Dhekelia and Larnaca, in Cyprus was assessed by microscopy-based classical taxonomy and eDNA metabarcoding. The results show impact of desalination brine discharge on marine benthic communities. The community structure and the impact of abiotic factors was more prominent in the sediments than the water, and the alpha diversity results from metabarcoding were consistent with the results from microscopy but differed taxonomically.