Despite growing interest in phylogenetic and functional methods in ecological assembly, less attention has been paid to seasonal variation patterns of migrant species. Migrants can rapidly mediate influences of species interactions and environmental factors through seasonal movement, suggesting dynamical relative importance of different assembly mechanisms among seasons. Here we describe seasonal dynamics in phylogenetic and functional diversity of waterbirds in Mai Po Wetland, in a subtropical region with significant predictable temporal variation. Phylogenetic and functional structure of α diversity varied seasonally. Specifically, phylogenetic structures clustered in summer, while being over-dispersed in winter. However, phylogenetic structure in spring and autumn was intermediate with a transition to random. Functional structure was clustered in spring but showed over-dispersion in the other three seasons. For β diversity, summer and winter assemblages had two distinct groups, while spring and autumn assemblages were mixed. Thus, waterbird assemblages were primarily shaped by interspecific competition in winter. Random processes tended to shape assemblage in spring. Environmental factors played a more important role in summer . In addition, phylogenetic distance of probability of co-occurrence of species pairs was significantly larger in winter than in summer. These results suggest that the relative importance of assemblage mechanisms can vary seasonally in response to changing environmental conditions, suggesting that studies attempting to infer a single dominant assembly mechanism may ignore important assembly processes. Temporal shifts in assembly mechanisms may play an important role in maintaining diversity of subtropical and temperate wetlands and perhaps other dynamic systems.