River-floodplain ecosystems are highly complex and dynamic systems that are subjected to human disturbance, such as the construction of levees. Aquatic insects are among the most widely used indicators to assess human impacts on floodplain wetlands. Most studies are still based on taxonomic biodiversity. However, trait-based approaches remain limited, which could impede the development of effective management strategies. Here, we investigated aquatic insect assemblages in eleven pairs of wetlands along the Wusuli River in two seasons (Spring and Autumn) and assessed their responses to the impact of levee construction, considering taxonomic and functional diversity. We found that pooled species richness (73 taxa) in river-connected wetlands was almost twice of that in levee-blocked wetlands (37 taxa). Six and one indicator taxa for river-connected wetlands were identified in May and October, respectively, while no indicator taxon for the levee-blocked wetlands was identified. Moreover, taxonomic and functional alpha diversity in river-connected wetlands was much higher than in levee-blocked wetlands, but beta diversity showed a contrasting pattern. Additionally, multivariate dispersion analysis indicated a more evident difference in beta diversity between river-connected and levee-blocked wetlands in May than in October, likely due to the temporary lateral connection in summer (i.e., water flowed over levees during flood events). Our results revealed that anthropogenic impacts (e.g., levee construction and agricultural activity) weakened the connectivity of floodplain wetland ecosystems, leading to decreased taxonomic and functional diversity of aquatic insects in isolated wetlands. Our study highlights the importance of combining taxonomic and trait-based approaches in biomonitoring programs of floodplain wetland ecosystems. It also underscores the necessity of restoring habitat connectivity of wetland ecosystems (e.g., river-floodplain connectivity and connections between different wetlands) to facilitate biodiversity recovery and enhance ecological functions and services supported by these valuable ecosystems.