The metacommunity framework has greatly advanced our understanding about the importance of local and regional processes structuring ecological communities. However, information on how metacommunity structure and the relative strengths of their underlying mechanisms change through time is largely lacking. Dynamic systems that undergo environmental temporal changes and disturbances, such as floodplains, serve as natural laboratories to explore how their metacommunity structure change in time. Here we applied the Elements of Metacommunity Structure framework and variation partitioning analysis to assess how temporal changes in the local environmental factors and regional dispersal processes in the rain season influence a seasonal floodplain-fish metacommunity. Across four months, relevant environmental factors were measured across 21 patches where over 3500 individual fish were sampled. Connectivity was measured using landscape resistance-based metrics and additional spatial variation in metacommunity structure was assessed via spatial autocorrelation functions. The metacommunity structure changed from nestedness, at the beginning of the flood season, to a quasi-Clementsian gradient at the end. Our analyses show that connectivity is only important in the beginning of the flood season whereas environment is only important at the end. These results suggest that this metacommunity is structured by changes between dispersal limitation and environmental filtering through time.