With seawater desalination expanding rapidly, it is important that ecological studies are undertaken to determine the effects of brine discharge on the marine species in the area. The abundance of giant Australian cuttlefish (Sepia apama, Gray 1849) eggs and environmental data were recorded at nine sites near Point Lowly, Spencer Gulf, South Australia, an area where the largest desalination plant in the Southern hemisphere is proposed. In addition, the effects of different concentrations of desalination brine on the growth, survival and condition of cuttlefish embryos were investigated. The primary egg-laying sites for the cuttlefish were in the vicinity of Stony Point (sites 4 and 3) and the area with the least egg abundance was on the eastern and western areas around Point Lowly (sites 9 and 7) where no eggs were found. The survival of embryos decreased with an increase in salinity, with no embryos surviving to full term in salinities greater than 50 per thousand. Mean weight and mantle length also decreased with increasing salinity. Besides elevated salinity, the brine also had increased concentrations of Ba, Ca, K, Sr and Mg relative to water near Point Lowly. Brine discharge from seawater desalination poses a potential threat to the unique spawning aggregation of the giant Australian cuttlefish, in the upper Spencer Gulf, South Australia.