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Metacommunity structure can be shaped by a variety of processes operating at different spatial scales. With increasing scale, the compositional variation among local communities (beta diversity) may reflect stronger environmental heterogeneity, but may also reflect reduced exchange of organisms between habitat patches. We analyzed the spatial architecture of a metacommunity of cladoceran zooplankton in temporary pools of High Andes wetlands, with the objective of explaining the spatial dependency of its structure. The spatial distribution of the pools is hierarchical and highly discontinuous: pools are clustered within small wetlands, which lay scattered over valleys that are separated from each other by mountain ridges. We studied a total of 59 pools, belonging to six different wetlands in four different valleys. We assessed pool environmental heterogeneity and sampled active communities and dormant propagule banks of cladoceran zooplankton. Environmental heterogeneity proved very high within wetlands and showed almost no increase with increasing spatial scale. Conversely, diversity partitioning analyses indicated an increase in beta diversity with spatial scale, especially among valleys. Variation partitioning on environmental data and spatial RDA models suggested environmental heterogeneity as the most important generator of beta diversity within wetlands. At the largest spatial scale, beta diversity manifested itself mainly as a differentiation of species occurrence patterns among valleys, which could not be entirely explained by environmental variables. Our study thus presents a case where environmental control seems to be the dominant metacommunity structuring process at the smallest spatial scale, whereas neutral processes and dispersal limitation are the most likely generators of beta diversity at the largest spatial scale.