The secondary salinisation of wetlands is a global problem that poses a profound threat to freshwater biodiversity. We examined wetland use by diurnal birds in relation to wetland salinity in the Wimmera region of south-eastern Australia to better understand the threat posed to biodiversity by secondary salinisation. Forty species of birds were detected in 66 non-riverine wetlands that spanned the broad range of salinities encountered among wetlands in the study region. Use of wetlands by birds was related to conductivity of water using a statistical model that accounted for imperfect detection of bird species during the surveys. Of the 40 species encountered during the study, it was estimated that 20 (95% credible interval 17–24) would respond positively to increasing salinity, and 20 (95% credible interval 16–23) would respond negatively to increased salinity. Expected species numbers are highest in wetlands of intermediate salinity. Our results accord well with our existing understanding of wetland use and salinity for most bird species we encountered, and show that expected future increases in wetland salinity are likely to dramatically alter patterns of wetland use by birds.