Intermittent wetlands are particularly at risk from secondary salinisation because salts are concentrated during drawdown. We conducted a field experiment to examine the effect of adding salt at two different concentrations (to achieve nominal conductivities of 1000 μS cm^–1 (low salt) and 3000 μS cm^–1 (high salt)) on water quality, freshwater plants and epiphytic diatoms in an intermittent wetland during a 3.3-month drawdown. Conductivity increased to 3000 and 8500 μS cm^–1 in low-salt and high-salt treatments respectively. Salt was apparently lost to the sediments, causing protons to be released from the sediments and reducing water column pH from 6.9 to 5.5 in the low-salt treatment and to 4.0 in the high-salt treatments. Forty days after adding the salt, biomass, %cover and flower production in Potamogeton cheesmanii were significantly reduced, whereas Amphibromus fluitans was not significantly affected. The salt effect on Triglochin procera was intermediate between the other two macrophytes. Significant reductions in the density, species richness and diversity of epiphytic diatoms occurred in the high-salt, but not in the low-salt, treatments. Our work shows that increases in salinity, and thus conductivity (up to 8500 μS cm^–1), in low-alkalinity intermittent wetlands can change water quality, with significant adverse effects on some macrophyte and diatom communities.