Global climate models predict future temperature and precipitation conditions that will increase the likelihood of unpredictable drought in currently perennially-flowing stream ecosystems. In this study, an experiment using artificial streams examined the impact that unpredictable desiccation and rehydration have on lotic periphyton community structure. 23 day-old periphyton communities were slowly desiccated and rehydrated over the course of two weeks, and changes in cell density and community composition were analyzed. Results indicated that a catastrophic loss of cell density occurred during desiccation, as most diatoms were eliminated and blue-green and green algal densities were severely depressed. The remaining desiccated periphyton community was dominated by blue-green, and to a lesser extent, green algae. After a 24-hour rewetting period, a 3-fold increase in cell density occurred and blue-greens continued to dominate the community. Immigration analysis indicated that immigrant cells could not have been solely responsible for the increase in cell density, suggesting that reproduction was more important during recovery. Cell health data revealed unique kingdom-specific responses to desiccation: diatom cells were empty, green algae exhibited some cellular damage, and blue-green algal cells were mostly healthy. The results of this study suggest that in streams that lack any history of seasonal desiccation, catastrophic loss of all periphyton occurs during drought, but blue-green and green algae are relatively better at surviving and recovering from desiccation than diatoms.