We investigated the temporal variations of periphyton communities at three sampling sites in coastal river with different contamination levels in the Shanghai Pudong New Area using High Throughput Sequencing (V4 region of 18S rDNA). A total of 36 samples were collected, and 30 phyla and 681 genera of periphyton were identified including Pentatrocha, Philodina, Vorticella, Physocypria, etc. The composition of periphyton communities in rivers varied significantly with different contamination levels. The community structure of the periphyton communities changed significantly during the survey period, and the community succession in the river sections with different levels of contamination showed differences. The abundance of arthropods at site H decreased rapidly after a sudden increase, while the ciliate dominance decreased dramatically and the chlorophyta became dominant at both sites H and Y during the late sampling period. RDA analysis showed that salinity significantly affected the periphyton communities. Different dominant groups responded differently to environmental changes, such as Pentatrocha, Philodina and Vorticella. This study will provide basic data to further understand the diversity and spatial and temporal succession of periphyton in coastal river and to conduct ecological health assessment of periphyton in damaged water bodies.