【Aim】 To investigate the biodiversity of shellfish and shrimp and analyze their ecological risks in the typical waters of Beijing. 【Method】 Five rivers, including the North Canal, Chaobai River, Yongding River, Daqing River, and Jiyun River, and typical waters along the South-to-North Water Transfer Project in Beijing, were selected and monitored three times in June, August, and October 2020. A total of 48 monitoring sites were surveyed, covering all water types, including rivers, lakes, and reservoirs. Through the classification and identification of collected samples, the species composition, distribution, characteristics, and biodiversity of shellfish and shrimp were analyzed, and the ecological risk of potential invasive species was preliminarily analyzed. 【Result】 A total of 27 species of shellfish and shrimp belonging to 13 families were identified, including 22 species of shellfish belonging to 11 families and five species of shrimp belonging to two families. The dominant species at all the monitoring sites for the three sampling dates were Bellamya angularia, Parafossarulus striatulus, Neocaridina denticulata sinensis, and Bellamya aeruginosa. The species number, density, and biomass of shellfish and shrimp increased first and then decreased in all the sampling sites from June to October, whereas the biodiversity showed a continuous increase trend. From the perspective of water type, the species composition and biodiversity of shellfish and shrimp at the various sites did not show significant differences. The homogenization trend was obvious for all species, whereas the biomass and density of shellfish and shrimp in lake-type water were higher. In addition, living samples of the invasive golden mussel Limnoperna fortunei were collected at two sites, Yuyuantan and Longtanzha, and the densities of this species at these sites were higher than those of other species during the three monitoring periods, indicating that the biological invasion risk of L. fortunei in the Beijing area was high. Continuous surveillance is urgently needed, and close attention should be paid to the population density of invasive L. fortunei. 【Conclusion】 The resources of benthic animals, especially shellfish and shrimp, are abundant in the Beijing area, but relevant monitoring surveys have not fully covered the local shellfish and shrimp species. Monitoring efforts should be strengthened in follow-up work, and the population dynamics and invasion of the invasive species of L. fortunei should be closely monitored.