In arid and semiarid regions, extreme temperature events and the frequency and duration of drought will increase toward 2050, leading to increased salinisation of inland waters, aggravated by catchment erosion and human activities (e.g., crop irrigation). With salinisation, a decline in biodiversity is expected, with potential negative effects on food web structure and ecosystem dynamics. Our objective was to assess the changes in community and food web structure in 24 lakes along a wide salinity gradient (i.e., subsaline to hypersaline) in a semiarid region in northwest China. Fish, zooplankton, and macroinvertebrate communities were sampled for taxonomic determination, size structure, and stable isotope analysis (SIA; delta C-13 and delta N-15). Based on SIA, we calculated the Layman metrics: nitrogen range, carbon range, total area, standard ellipses area, and the trophic position, for each community and for the entire food web. We found a reduced number of taxa of all analysed communities, and the complexity of the entire food web decreased in most saline lakes. In addition, the trophic diversity and trophic position declined, less so in the larger lakes, but these effects were not significant when studying the community food webs separately. Our results suggest that increasing salinisation with ongoing climate warming will have negative effects on lake ecosystems in arid and semiarid regions, emphasising the need to implement management measures at the watershed level to prevent or mitigate future changes in food web structure and biodiversity due to salinisation.