The boreal landscape is a mosaic of wetlands with distinct ecosystem properties. Algae are important for wetland functioning, but relatively little is known about the structure of algal communities among boreal wetlands. We documented spatial and temporal variability of algal community dynamics and productivity during a growing season in 6 wetlands (1 rich and 1 poor fen, 1 tussock, and 3 riverine marshes) in interior Alaska. Algal biomass and productivity were greater in the poor fen and a riverine marsh than in all other wetlands. Water depth and nutrients were significant predictors of benthic algal biomass and productivity among wetlands and were greatest immediately after the spring thaw and decreased during the growing season. Water depth and nutrients (N and P) explained the most variability in algal community structure. Algal community structure differed among wetlands, and temporal variation in environmental conditions was a significant predictor of the relative abundance of algal genera in individual wetlands. N₂-fixing cyanobacteria increased in abundance with a seasonal decline in water depth and nutrient concentrations. Our characterization of algal community dynamics and productivity in relation to environmental characteristics will help to forecast future wetland function in a changing boreal landscape.