Both habitat heterogeneity and disturbance can profoundly influence ecological systems at many levels of biological and ecological organization. However, the joint influences of heterogeneity and disturbance on temporal variability in communities have received little attention despite the intense homogenizing influence of human activity. I performed a field manipulation of substrate heterogeneity in a small New England stream, and measured changes in benthic macroinvertebrate communities for 100 days—a period that included both a severe drought and a flood. Generally, community variability decreased with increasing substrate heterogeneity. However, within sampling intervals, this relationship tended to fluctuate through time, apparently tracking changes in hydrology. At the beginning of the experiment, community temporal variability clearly decreased along a gradient of increasing substrate heterogeneity—a result consistent with an observational study performed the previous year. During the subsequent weeks, droughts and flooding created exceptionally high variability in both hydrology and benthic macroinvertebrate community structure resulting in the disappearance of this relationship. However, during the last weeks of the experiment when hydrologic conditions were relatively more stable, the negatively sloped relationship between community temporal variability and habitat heterogeneity reemerged and mimicked relationships observed both early in the experiment and in the previous year’s study. High habitat heterogeneity may promote temporal stability through several mechanisms including stabilization of resources and increased refugia from minor disturbances or predation. However, the results of this experiment suggest that severe disturbance events can create large-scale environmental variability that effectively swamps the influence of habitat heterogeneity, illustrating that a thorough understanding of community temporal variability in natural systems will necessarily consider sources of environmental variability at multiple spatial and temporal scales.