The Arctic Ocean is subject to severe environmental changes, including the massive decline in sea ice due to continuous warming in many regions. Along with these changes, the Arctic Ocean’s ecosystem is affected on various scales. The pelagic microbial food web of the Arctic is of particular interest, because it determines mass transfer to higher trophic levels. In this regard, variations in the size structure of the microbial community reflect changes in size-dependent bottom-up and top-down processes. Here we present analyses of microscopic data that resolve details on composition and cell size of unicellular plankton, based on samples collected between 2016 and 2018 in the Fram Strait. Using the Kernel Density Estimation method, we derived continuous size spectra (from 1μm to ≈ 200 μm Equivalent Spherical Diameter, ESD) of cell abundance and biovolume. Specific size intervals (3–4, 8–10, 25–40, and 70–100 μm ESD) indicate size-selective predation as well as omnivory. In-between size ranges include loopholes with elevated cell abundance. By considering remote sensing data we could discriminate between polar Arctic- and Atlantic water within the Fram Strait and could relate our size spectra to the seasonal change in chlorophyll-a concentration. Our size spectra disclose the decline in total biovolume from summer to autumn. In October the phytoplankton biovolume size-spectra reveal a clear relative shift toward larger cell sizes (>30μm). Our analysis highlights details in size spectra that may help refining allometric relationships and predator-prey dependencies for size-based plankton ecosystem model applications.