The development and reconciliation of the neutral and niche theories helped us understand community assembly, yet little is known about the relative importance of neutral and niche processes across time and space. We utilized tree-hole communities in a seasonal tropical forest of Xishuangbanna, China, to test how these processes influence the community assembly of tree-hole aquatic microcosms in the forest canopy and understory across seasons. Tree-holes of reasonable sizes can hold a small quantity of water, harboring relatively diverse communities with food webs, including scavengers and predators, providing an ideal platform to study community ecology. Plastic containers were used to create fully standardized tree-hole microcosms. We hypothesized that deterministic (niche) processes are stronger in the canopy than understory communities, especially during the dry seasons, due to the highly exposed nature of canopy microhabitats. Unlike our hypothesis, canopy communities were highly stochastic in the dry season, whilst deterministic processes prevailed in the wet seasons. The understory community assembly was highly stochastic regardless of seasons. The lack of interspecific interactions suggests that environmental rather than interspecific interactions drive such deterministic processes. Our study demonstrated that seasonality could shift the community assembly processes, but the presence of forest canopies can buffer this.