Traditionally metacommunity studies have quantified the relative importance of dispersal and environmental processes on observed β-diversity. Separating β-diversity into its replacement and nestedness components and linking such patterns to metacommunity drivers can provide richer insights into biodiversity organization across spatial scales. It is often very difficult to measure actual dispersal rates in the field and to define the boundaries of natural metacommunities. To overcome those limitations, we revisited an experimental metacommunity dataset to test the independent and interacting effects of environmental heterogeneity and dispersal on each component of β-diversity. We show that the balance between the replacement and nestedness components of β-diversity resulting from eutrophication changes completely depending on dispersal rates. Nutrient enrichment negatively affected local zooplankton diversity and generated a pattern of β-diversity derived from nestedness in unconnected, environmentally heterogeneous landscapes. Increasing dispersal erased the pattern of nestedness, whereas the replacement component gained importance. In environmentally homogeneous metacommunities, dispersal limitation created community dissimilarity via species replacement whereas the nestedness component remained low and unchanged across dispersal levels. Our study provides novel insights into how environmental heterogeneity and dispersal interact and shape metacommunity structure.