Physical and chemical data collected in the Canada Basin interior from 2003–2009 show that recent increases in both Ekman convergence and freshwater input, associated with sea ice retreat and melt, have affected the structure and dynamics of the upper ocean, and such changes accelerated from 2007–2009 when salt-stratification below the seasonal mixed layer increased about 25%. This increased stratification further constrains vertical heat flux and the winter renewal of nutrients into the euphotic zone. One consequence of increased convergence is that both the depth of the nitracline (i.e. the depth where nitrate concentrations begin to increase from zero) and the depth of the chlorophyll maximum (which occurs slightly below the depth of the nitracline as here both nitrate and light are sufficient to allow primary production) have increased. Nitrate concentrations at the chlorophyll maximum depth have also recently decreased which suggests that the availability of light may play a progressively greater role in determining the depth at which primary production occurs. If these trends continue, assuming that the depth of the winter mixed layer does not deepen, such changes will negatively affect primary productivity as long as the Arctic Oscillation remains anticyclonic and freshwater continues to be stored in the Beaufort Gyre. These findings show that, under such conditions, the response of sea ice retreat in the basin interior is distinct and opposite to the response on adjacent continental shelves where shelf-break upwelling will increase, bringing nitrate into the euphotic zone and enhancing production.