Connectivity, a fundamental concept in ecology, refers to the extent to which different habitats or ecosystems are interconnected through the movement of organisms, nutrients, and energy. Lateral hydrological connectivity (LHC) plays an especially critical role in shaping aquatic community organization in river-floodplain systems. However, a comprehensive understanding of various trait responses to LHC remains elusive. We characterized how attributes of fish community traits, specifically composition, divergence, and temporal variability respond to LHC in the Austrian-Hungarian floodplains of the Danube River using environmental DNA (eDNA) metabarcoding. Trait composition was quantified by community-level weighted means (CWM) as the degree of changes in trait responses along the LHC gradient from isolated oxbows to the main river. Divergence was measured using Rao’s quadratic functional diversity index and a null model approach to calculate standardized effect sizes (SES), with larger SES values indicating greater divergence and smaller values indicating convergence. Temporal variability, representing the degree of instability in community traits over time, was calculated using a functional beta diversity measure for multiple communities. Our findings revealed apparent compositional changes for many trait variables, highlighting the significance of LHC in shaping community functional diversity. Divergence patterns indicated that isolated habitats foster trait convergence presumably due to habitat filtering, whereas more connected areas promote trait divergence due to higher species richness and habitat availability. Temporal variability of traits associated with flow preference exhibited a hump-shaped relationship with LHC, suggesting intermediate connectivity zones are hotspots of ecological dynamism. The study suggests that examining composition, divergence, and temporal variability together provides a more complete understanding of trait responses to connectivity, stressing the importance of maintaining diverse connectivity levels in river-floodplain systems for effective conservation and ecosystem management.