Fish diversity, an important indicator of the health of aquatic ecosystems, is declining sharply due to water pollution, overfishing, climate change, and species invasion. Effective surveying and monitoring are prerequisites for protecting fish diversity. In this study, eDNA (environmental DNA）metabarcoding and ground cages were used to survey the fish diversity of the Chaobai and Beiyun Rivers in Beijing. Based on the two methods, the results showed that 40 species, belonging to 35 genera, 18 families, and six orders, were identified. The richness of fish identified by eDNA metabarcoding was higher than that captured by ground cages in both rivers. All fish captured by the ground cage method were recognized by eDNA metabarcoding, except Squalidus wolterstorffi and Saurogobio dabryi, which were captured only in ground cages. The correlation of relative abundance between the two methods was affected by the properties of the rivers, such as the flow rate. The relative abundance detected by eDNA metabarcoding was positively correlated with that of the ground cages in the Beiyun River, while no correlation was observed for the Chaobai River. Our results also suggest that the Chaobai River has higher fish diversity and a different population structure than the Beiyun River. The primary fish species of the Beiyun River are mainly pollution resistant. This results show that eDNA metabarcoding as a new survey tool has great application prospects. It provides certain theoretical data and methodological references for the protection and management of river fish diversity.