Phytoplankton species composition and the associated community size structure are expected to change with a warming and freshening of the Arctic Ocean. Cell size controls many physiological (bottom-up) processes, such as nutrient uptake, photosynthesis and growth, thereby affecting the functioning of the planktonic ecosystem as a whole. Furthermore, predator-prey interaction (top-down control) is highly size dependent. The size structure of the phytoplankton community in the Fram Strait has been analysed, based on observations of cell abundance and size. Non- parametric size spectra are obtained from microscopic observations, using a statistical approach that also provides respective confidence intervals. A bootstrap approach is applied, with cell counts and size measurements being resampled respectively. Kernel density estimates (KDE) are derived for all resampled data sets. The collection of KDEs yield robust continuous descriptions of cell density versus cell size together with their confidence limits. With this approach we resolve detailed changes in community size structure that shall be used to improve and constrain results of a size-based plankton ecosystem model. Size dependencies of bottom-up and top-down effects on biogeochemical mass flux will be investigated. The calibrated model can then be applied for deriving reliable projections of how the planktonic ecosystem in the Arctic may be affected by climate change.