We investigated the ecological effects of salinity mitigation strategies in the Murray-Darling Basin (MDB) using macroinvertebrate data collected over 2,300 km of the Murray River between 1980 and 2012. The MDB covers 1 × 106km2 and includes both temperate and semiarid climate zones. It was extensively developed to support irrigated agriculture in the early to mid-1900s, and the secondary salinization that followed has become a major concern. During 1975–1985 daily salinity levels, measured as electrical conductivity above the Murray River off-take points for South Australia's major urban water supplies, were above 800 μS/cm for 40% of the time, necessitating mitigation strategies that have reduced the average salinity by about 150 μS/cm since monitoring began. The MDB has also experienced several major floods and droughts during this time, and surface temperatures in the MDB have increased by 0.8 °C since 1910, mostly in the last 50 years. We hypothesized that (1) taxa richness would increase in response to floods; (2) community structure would shift toward tolerant, opportunistic taxa in response to warming; and (3) geographical ranges of species would change in response to shifting stream isotherms and reducing salinity. Our hypotheses were supported, although increases in water temperature appeared to be due principally to the 1997–2009 Millennium drought. Importantly, against a backdrop of significant climate variability, we believe we have distinguished a change in community structure along a salinity gradient and that changes over the 33 years can in part be attributed to mitigation strategies.