Highly saline brines from desalination plants expose seagrass communities to salt stress. We examined effects of raised salinity (46 and 54 psu) compared with seawater controls (37 psu) over 6 weeks on the seagrass, Posidonia australis, growing in tanks with the aim of separating effects of salinity from other potentially deleterious components of brine and determining appropriate bioindicators. Plants survived exposures of 2–4 weeks at 54 psu, the maximum salinity of brine released from a nearby desalination plant. Salinity significantly reduced maximum quantum yield of PSII (chlorophyll a fluorescence emissions). Leaf water potential (Ψw) and osmotic potential (Ψπ) were more negative at increased salinity, while turgor pressure (Ψp) was unaffected. Leaf concentrations of K+ and Ca2 + decreased, whereas concentrations of sugars (mainly sucrose) and amino acids increased. We recommend leaf osmolarity, ion, sugar and amino acid concentrations as bioindicators for salinity effects, associated with brine released in desalination plant outfalls.