We examined the determinants of zooplankton and phytoplankton metacommunity structure across 25 boreal wetland ponds. Our objective was to determine whether plankton metacommunities exhibit spatial structuring, thus suggesting neutrality, or are merely structured by local environmental features, suggesting that they are under niche-based control. According to Redundancy Analysis (RDA), zooplankton community structure was primarily controlled by concentration of major ions and geographical location of the pond, while phytoplankton community structure was primarily controlled by major ion concentration, nitrogen concentration, and geographical location. According to variance partitioning in RDA, zooplankton community structure was attributed more to pure spatial position of the pond (16.7% of variance) than to pure environmental factors (4.7% of variance). For phytoplankton, community composition was controlled by both spatial and environmental factors, although the effect of pure spatial position (11.1% of variance) on phytoplankton community structure was somewhat weaker than for zooplankton. For zooplankton, community similarity was negatively (P < 0.01) related to both geographical and environmental distance. For phytoplankton, community similarity was negatively (P < 0.05) related only to geographical distance. Finally, cluster analyses showed that zooplankton and phytoplankton communities formed highly dissimilar groupings, thus implying low community concordance. Our results suggest that both zooplankton and phytoplankton comply with both neutral and niche-based models. Our results further imply that even across small spatial scales and even for small organisms such as plankton, communities might be strongly spatially structured. The finding that spatial configuration was even more important than local environmental factors in controlling zooplankton community composition suggests that zooplankton may be dispersal-limited within relatively small spatial scales or that zooplankton metacommunities might be related to mass effects.