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Caves represent unique and extreme ecosystems inhabited by specifically adapted and metabolically diverse organisms (phototrophs, heterotrophs, and mixotrophs). Hydrogeologically active river caves, such as Stopić Cave (Serbia), have additional characteristics. Knowledge is lacking on the cyanobacteria and algae living in these specific ecosystems and, in particular, in the water bodies within caves. The main objectives of this study were to investigate the diversity, composition, and seasonality of cyanobacterial and algal communities of the Trnavski stream flowing through Stopić Cave and to assess water quality. Initial analysis of planktonic and benthic samples collected during the winter, spring, and summer of 2020 from six sites along the Trnavski stream flowing through Stopić Cave identified 132 cyanobacterial and algal taxa. Subsequent detailed analysis of benthic diatoms increased the total number of identified taxa to 242, with representatives of Bacillariophyta, Cyanobacteria, and Chlorophyta being the most common. Representatives of Xanthophyceae, Chrysophyceae, Euglenophyceae, Dinophyceae, and Cryptophyceae were also recorded. The highest total number of taxa was found in the spring (n = 156), and the lowest number in the summer (n = 60). Many taxa were specific to only one season, with the majority of these belonging to Cyanobacteria and Chlorophyta. The values recorded for pH, conductivity, and light intensity showed that there was relatively little seasonal variation; in contrast, water temperature varied greatly among seasons. According to most diatom indices, the water quality of Trnavski stream was good at most sampling sites during the study period. [ABSTRACT FROM AUTHOR]