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We quantified phytoplankton growth and protistan grazing rates during late austral autumn 2013 and late austral spring 2014, in several glacio‐marine fjords and connecting channels along the Western Antarctic Peninsula (WAP). During austral autumn, low and declining chlorophyll a (Chl a) concentrations (≤ 0.4 μg L−1) were almost entirely composed of pico/nanophytoplankton, whereas during austral spring, high but patchy Chl a concentrations in the fjords (up to 18.5 μg L−1) reflected a diatom bloom. These contrasting dynamics were associated with high seasonal differences in irradiance, but not temperature, and were consistent with the balance resulting from lower phytoplankton growth rates in autumn (−0.01 d−1 to 0.19 d−1) than in spring (0.06–0.93 d−1) but similar magnitudes of herbivorous grazing in both seasons. Grazing was either absent or low (0.11–0.26 d−1) and restricted to the picophytoplankton and nanophytoplankton. In the productive fjords lining the WAP, a fraction of primary production was channelled through a persistent and across‐seasons equally active microbial food web, while during spring an increasing fraction of organic carbon shifted from trophic transfer and recycling to an export pathway. [ABSTRACT FROM AUTHOR]