The anthropogenic salinisation of rivers causes grave environmental problems that are responsible for the degradation of water quality on a worldwide scale as well as for biological changes in aquatic ecosystems. The objectives of the survey were to analyse the structure of the macroinvertebrate communities in the Bolina River, which is currently the second most anthropogenic salinised river in the world, in relation to various types of instream microhabitats and to determine the environmental factors that have a significant effect on the structure of the macroinvertebrate communities. The result of a canonical correspondence analysis (CCA) showed that electrical conductivity, the temperature of the water and the organic matter content in the bottom sediments were the most important factors (statistically significant) that influenced the macroinvertebrate communities in the anthropogenic salinised river. A total of 77 taxa of macroinvertebrates were recorded in the Bolina River. A Kruskal-Wallis one-way ANOVA and multiple comparison post hoc tests revealed statistically significant differences in the median number of taxa and the median density of macroinvertebrates between the various types of microhabitats in the salinised river. The anthropogenic salinisation of a river can lead to a decrease in aquatic biodiversity that favours invasive species over native species. The Bolina River, which has a salinity of up to 33.6‰, is an example of a unique habitat for organisms that are salt tolerant (euryhaline) or eurytopic. It is a route for the spread of alien and invasive invertebrate species including Gammarus tigrinus, Potamopyrgus antipodarum, and Monopylephorus limosus.