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Assessments of carbon and nitrogen (N) assimilation in Canadian Arctic waters confirmed the large contribution of subsurface chlorophyll maxima (SCM) to total water-column production from spring to late fall. Although SCM communities showed acclimation to low irradiance and greater nitrate (NO<sub>3</sub><sup>−</sup>) availability, their productivity was generally constrained by light and temperature. During spring–early summer, most of the primary production at the SCM was sustained by NO<sub>3</sub><sup>−</sup>, with an average <i>f</i>-ratio (i.e., relative contribution of NO<sub>3</sub><sup>−</sup> uptake to total N uptake) of 0.74 ± 0.26. The seasonal decrease in NO<sub>3</sub><sup>−</sup> availability and irradiance, coupled to the build up of ammonium (NH<sub>4</sub><sup>+</sup>), favoured a transition toward a predominantly regenerative system (<i>f</i>-ratio = 0.37 ± 0.20) during late summer and fall. Results emphasize the need to adequately consider SCM when estimating primary production and to revisit ecosystem model parameters in highly stratified Arctic waters.