Floristic studies indicate the abundance of microalgae in northern boreal peatlands, but we know relatively little about their ecology or how they will respond to changes in environmental conditions expected in this region as climate changes. We examined changes in algal community structure at sites exposed to a long-term water-table manipulation, including drought (lowered water-table treatment), flooding (raised water-table treatment), and control (no manipulation) treatments in an Alaskan fen. In previous years, continuous algal colonization typically would have occurred only in the raised water-table treatment, but a spring flood inundated experimental plots and provided a unique opportunity to examine algal community response to rewetting after long-term drought. This event allowed us to investigate how much ecosystem memory of the antecedent water-table manipulations regulated the ability of taxa to recolonize sites after prolonged drought compared to sites that had been continuously flooded. Despite no differences in water-table position among treatments at the time of sampling, surface-water nutrient concentrations were higher in the lowered water-table treatment relative to the other treatments after the spring thaw. This difference corresponded with greater algal abundance and biovolume in the lowered water-table treatment relative to the control and raised water-table treatments. Higher abundance and biovolume was driven mainly by filamentous green algae (Chlorophyta), especially Oedogonium, Spirogyra, and Microspora. Diatoms were most abundant in the raised water-table treatment, whereas chrysophytes were most abundant in the control treatment. Across all water-table treatments, N-fixing cyanobacteria increased as nutrients and water-table position declined over time. The differences in algal community structure among water-table treatments suggest that alternating drought and flooding events expected with climate change may significantly alter algal-driven functions in boreal wetlands.