Understanding seasonal patterns of assembly mechanisms are key to comprehending the metacommunity dynamics of organisms inhabiting temporary habitats such as wetland macroinvertebrates. However, tests of the seasonal variation in assembly mechanisms of macroinvertebrates in wetlands with differing hydroperiods are rare, especially in the Neotropical region. We tested for seasonal patterns in the metacommunity assembly mechanisms of macroinvertebrates in small subtropical highland wetlands of southern Brazil with different hydroperiods. We also tested whether patterns varied between macroinvertebrate taxa with different dispersal modes. Macroinvertebrates were sampled in 12 wetlands classified into "short," "medium," and "long" hydroperiods (N = 4 in each category) in three seasons (fall, winter, and spring) over two full hydrological cycles (from 2012 to 2014). We assessed the role of spatial and environmental variables to metacommunity structure using distance‐based redundancy analysis and variation partitioning. Environmental and spatial variables explained macroinvertebrate metacommunity structure, although their relative influence markedly changed among seasons and hydroperiods. Environmental variables were important in fall and winter, whereas spatial variables predominated in spring. Different environmental variables influenced the metacommunity structure in each hydroperiod. Environmental variables influenced active‐dispersing macroinvertebrates, whereas the influence of environmental and spatial variables on passive‐dispersing taxa changed among seasons. We showed that the assembly mechanisms of macroinvertebrate metacommunities show a distinct temporal dynamic among wetlands with different hydroperiods. Our findings contribute to a more complete understanding of the metacommunity structure in temporary ecosystems. [ABSTRACT FROM AUTHOR]