BackgroundAlgae play important roles in urban river ecosystems and are the cornerstones of most water quality monitoring programs. Thus, a better understanding of algal community dynamics is needed to support sustainable management of water resources in urban rivers.ResultsIn this study, we quantified the seasonal variations in planktonic and periphytic algal community structure in the highly urban Fenhe River and identified environmental factors affecting algal community structure and diversity. We monitored planktonic (drifting) and periphytic (attached) algal communities in the Taiyuan section of the Fenhe River over one year. The results indicated that Cyanophyta was the dominant phylum in both communities, followed by Bacillariophyta and Chlorophyta. Significant differences were observed in the composition of the planktonic and periphytic algal communities. In particular, the periphytic algal community was more diverse than the planktonic community. Water temperature and pH were the main environmental factors affecting planktonic and periphytic algal community structure, respectively, while nutrients were the most significant factor affecting planktonic and periphytic algal diversity. Ecological modeling indicated that the variations in the algal communities of the Fenhe River are mainly driven by stochastic processes. A co-occurrence network developed for the communities displayed positive interactions between the planktonic and periphytic algae.ConclusionsThese findings deepen our understanding of the seasonal interaction between planktonic and periphytic algae and the driving factors affecting community structure in the Fenhe River. They also provide a theoretical basis for the managing and protecting water resources in urban river ecosystems.