After much debate, there is an emerging consensus that the composition of many ecological communities is determined both by species traits, as proposed by niche theory, as well as by chance events. A critical question for ecology is, therefore, which attributes of species predict the dominance of deterministic or stochastic processes. We outline two hypotheses by which organism size could determine which processes structure ecological communities, and we test these hypotheses by comparing the community structure in bromeliad phytotelmata of three groups of organisms (bacteria, zooplankton, and macroinvertebrates) that encompass a 10 000-fold gradient in body size, but live in the same habitat. Bacteria had no habitat associations, as would be expected from trait-neutral stochastic processes, but still showed exclusion among species pairs, as would be expected from niche-based processes. Macroinvertebrates had strong habitat and species associations, indicating niche-based processes. Zooplankton, with body size between bacteria and macroinvertebrates, showed intermediate habitat associations. We concluded that a key niche process, habitat filtering, strengthened with organism size, possibly because larger organisms are both less plastic in their fundamental niches and more able to be selective in dispersal. These results suggest that the relative importance of deterministic and stochastic processes may be predictable from organism size.