Melosira Agardh and Aulacoseira Thwaites, which are widely distributed in freshwater basins, are an important part of phytoplankton under various nutrient conditions. In moderately-eutrophic waters, these organisms occupy a dominant position in the phytoplankton community, grow and reproduce rapidly, and even form blooms. Melosira Agardh connects two or three cells together through mucilage pads and small irregular spines on the valve faces, while Aulacoseira Thwaites is united at the valve faces by short, interlocking spines between sibling valves. These link the cells firmly together and then lead to filament formation. Some species of Aulacoseira Thwaites are easily distinguished from other species of Aulacoseira Thwaites or filamentous diatoms by the presence of long spines (also known as separation spines) on the terminal valves of the filaments. The Pearl River flows through the watershed of the Pearl River Delta into the South China Sea. In 2012 and 2015, we analyzed the spatiotemporal characteristics and influencing factors of filamentous diatoms in this area. A total of 18 species (including varieties and formas) of filamentous diatoms were observed, among which Aulacoseira granulata was the dominant species and an important indicator of eutrophication. The variation patterns of the total biomass during different water periods showed a large difference during the dry season and a small difference during the wet season, which was mainly influenced by the difference in runoff, transparency and water temperature. Spatially, the biomass of the stations around Guangzhou was obviously high, which was mainly a result of eutrophication. Based on the relative percentage of different filamentous diatoms, A. granulata was the dominant species, but Melosira varians formed a competitive advantage during dry season. The filament length of Aulacoseira was generally greater than that of Melosira, which was mainly because of its stable morphology. Transparency, nutrients, and pH were also important factors affecting filament length. Melosira Agardh and Aulacoseira Thwaites had the advantages of wide distribution, rich diversity, rapid and reliable response to changes in river water quality, fast reproduction, and easy location monitoring. These organisms are also known to be good indicators of environmental changes and are therefore commonly used as river water quality monitoring indicators in Europe and the United States.