We examined the light absorption properties and light-dependent rates of photosynthetic electron transport (ETRRCII) and 14C-uptake in phytoplankton of the Canadian Subarctic and Arctic Ocean. Our results reveal high variability in the light-saturated, chlorophyll a-specific rate of 14C-uptake (PChlamax; 0.7 to 8.0 mg C mg chl a−1 h−1), and the light-dependant efficiency of 14C-uptake (αChla; 0.01 to 0.09 mg C mg Chl a−1 h−1 [μmol quanta m−2 s−1]−1). Variability in PChlamax correlated with light availability in the stratified water-column, while both PChlamax and αChla were correlated to the degree of nitrate depletion in the mixed layer. For all samples, we observed that 14C-uptake rates reached light saturation at lower irradiances than ETRRCII, leading to significant, light-dependent de-coupling of carbon fixation and photosynthetic electron transport. For samples taken from within the mixed layer, we found that the conversion factor from ETRRCII to carbon fixation was strongly correlated to the magnitude of non-photochemical quenching, as derived from fast repetition rate fluorometry (FRRF) measurements. This correlation supports recent findings from the Subarctic Pacific Ocean, and has the potential to improve FRRF-based estimates of phytoplankton carbon fixation. Our observations reveal distinct environmental regulation of phytoplankton light absorption, electron transport and carbon fixation in phytoplankton assemblages within and below the shallow summer mixed layer, and will help to inform more robust predictions of future primary production in a rapidly changing Arctic Ocean.