The abundance of diatoms and heterotrophic bacteria in sea ice rapidly increases during the spring. However, the number and activity of these microorganisms vary with changing environmental conditions and potentially the taxonomic composition of the algal community during this time. In this study, we assessed the spring bottom-ice community composition in Dease Strait, Nunavut, and investigated potential controls of chlorophyll a (chl a), particulate organic carbon (POC), cell abundance, and production from early March until early June. We found that using flow cytometry to estimate photosynthetic nanoeukaryote (2–20 μm) abundance gave results very similar to light microscopy counts, except when pennate diatoms with lengths close to 20 μm, the maximum size detected by flow cytometry, were abundant. Using the average abundance of nanoeukaryotes from the two methods, we documented a change in the size of cells comprising the ice algal community over the spring, from largely pico- (<2 μm), to nano- and microeukaryotes (20–200 μm). This shift in ice algal size corresponded to a bloom in diatoms that drove increases in chl a, POC, and primary productivity. Low-salinity surface waters, limited nutrient availability, as well as seasonally intensifying light in the bottom ice appeared to support dominance of the centric diatom Attheya spp. Increases in the number and productivity of heterotrophic bacteria in this study were correlated with the number of photosynthetic picoeukaryote cells, potentially due to their supply of dissolved organic carbon substrate. Our results suggest that future conditions predicted for the Arctic that include low nutrients and greater light transmission to the bottom of sea ice may favor an ice algal community dominated by centric diatoms versus the more characteristic pennate diatom-dominated community.