All ecosystems experience some degree of environmental fluctuations. However, the nature of these fluctuations can vary drastically, from seasonal and daily shifts to multidecadal trends. Theory suggests that different components of environmental fluctuations can have distinct and even opposing effects on species’ abundances and community dynamics, depending on their specific adaptations. Here we use long-term macroinvertebrate monitoring data together with flow and water quality records of rivers across New Zealand to investigate the role of average, fast, slow, and seasonal river-flow fluctuations in structuring macroinvertebrate communities, and test whether life history and mobility traits mediate the response. We fit Joint Species Distribution Models via generalized linear latent variable models to simultaneously estimate species-specific responses, while accounting for residual correlations between species. We quantify environment-trait relationships through the fourth-corner approach. We found striking differences in species and community responses to the different components of river flow variation. In general, species' responses to seasonal fluctuations were highly heterogeneous, whereases fast increases in flow, typical of flooding events, had pervasive negative effects on species abundances. Life history and mobility traits did not explain much of the variability in species responses, with only the number of descendants showing a clear effect. Community-level responses imply that abundance gradients governed community changes against slow and fast flow fluctuations but balanced changes in species abundances were predominant in response to seasonal flow variability.