AbstractThe rapid physical changes affecting the Arctic Ocean alter the growth conditions of primary producers. In this context, a crucial question is whether these changes will affect the composition of phytoplankton communities, augment their productivity, and eventually enhance food webs. We combined satellite and model products with in situ datasets collected during fall and provide new insights into the response of phytoplankton biomass and production in the Canadian Arctic by comparing an interior shelf (Beaufort Sea) and an outflow shelf (Baffin Bay). Correlation analysis was used to distinguish between seasonal and interannual variability and revealed that most biological variables are responding to the interannual pressures of climate change. In southeast Beaufort Sea, a change in phytoplankton community composition occurred, with a significant increase in diatoms from 2% (2002) to 37% (2010–2011) of the total protist abundance. In 2011, photosynthetic picoeukaryotes were twice as abundant as in 2002. For these two phytoplankton groups, abundance was correlated with the duration of the open‐water period, which also increased and affected vertical stratification and sea‐surface temperature. In contrast, there was a sharp decline in centric diatom abundance as well as in phytoplankton biomass and production in northern Baffin Bay over the years considered. These decreases were linked to changes in seasonal progression and sea‐ice dynamics through their impacts on vertical stratification and freshwater input. Overall, our results highlight the importance of stratification and the duration of the open‐water period in shaping phytoplankton regimes—either oligotrophic or eutrophic—in marine waters of the Canadian Arctic.