Abstract: Understanding the distribution of chlorophyll on the continental shelves adjacent to western boundary currents is important, both from an ecosystem perspective, as well as for their role as a net sink of atmospheric CO2. However, in-situ observations of chlorophyll in these dynamic regions are rare. Here, using more than a decade of underwater glider observations from 29 deployments in the East Australian Current system, we examine the effect of the mesoscale western boundary current (WBC) circulation on chlorophyll distribution across the shelf. The gliders reveal that the mode of boundary current separation has a persistent spatial influence on both the stratification and chlorophyll distribution on the shelf between 31.5°S and 34°S. We identify that subsurface chlorophyll maxima are common, and their depth and strength is dictated by the offshore mesoscale circulation. Of the three dominant WBC separation scenarios, eddy dipoles result in shelf waters that are on average more stratified, have higher chlorophyll values, and a deeper chlorophyll maximum compared to other circulation modes. These results suggest that it is necessary to consider the influence of WBC dynamics on chlorophyll concentrations for accurate estimates of atmospheric CO2 uptake.