The occurrence and spread of halophilic diatom taxa in freshwater lotic ecosystems are influenced both by natural processes and anthropogenic pollution. Diatom assemblages were regularly monitored in lowland lotic systems in Hungary (Central Europe) during the unusually dry year of 2012. Highly pronounced changes in diatom composition were observed from spring to autumn. Halophilic taxa (especially Nitzschia sensu lato species) appeared in the dry autumn. In addition, the total relative abundances of halophilic species also increased up to autumn. Abundance of Nitzschia cf. lorenziana and Nitzschia tryblionella showed a positive correlation with chloride and phosphate concentration, while that of other taxa like Tryblionella apiculata or Tryblionella calida showed a positive correlation with the concentration of nitrate. Our findings clearly demonstrated that these halophilic and mesohalophilic diatom taxa were sensitive indicators of even short-term changes in lowland lotic ecosystems, such as the increasing salt concentration from spring to autumn caused by the lack of rainfall and/or environmental loads.