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We assess the potential of different forms of variation partitioning to distinguish between environmental control and dispersal limitation in communities structured by combinations of niche and neutral processes. Simulation data reveal interactions between dispersal limitation, environmental control, and the spatial structure of environmental factors in the detected levels of variance fractions. The degree of dispersal limitation contributes to both the pure environmental and pure spatial variance partitions. This undermines the common practice of interpreting these partitions as direct expressions of niche and neutral processes, respectively. Furthermore, the proportion of variation attributed to environmental variation depends not only on the strength of environmental control, but also on the specific spatial configuration of the environmental variable. This has important implications for the interpretation of empirical studies. In particular, use of these analytical techniques to compare processes governing community structure among different study systems is unwarranted, as the results will reflect not only differences in the strength of the processes of interest, but also the influence of the unique spatial arrangement of the environmental variables in each system.