Wetlands in south-eastern Australia and other arid regions of the world are experiencing increases in salinity due to dryland salinization and climate change. We investigated changes in wetland ecological function, measured as phytoplankton and benthic algal Chl a, over a large salinity gradient (0.047–226 mS cm⁻¹) and in relation to several local water chemistry variables that may be important predictors of algal biomass. We investigated the relative importance of landscape variables that may affect input pollution and hydrology of wetlands at four spatial scales (100, 500, 1,000 and 5000 m). We explored the strength and form of the relationships between algal biomass and local and landscape predictors with emphasis on the effects of local and landscape salinity. We found local variables were more important than landscape variables in influencing algal biomass. We also found salinity of wetlands was not a good predictor of phytoplankton biomass but it did predict benthic algal biomass.