Microalgae produce copious amounts of structurally diverse polysaccharides, some are bound within cells and cell walls, while others are secreted into the surrounding seawater. A fraction of the secreted polysaccharides assembles into particles promoting aggregation and in turn formation of aggregates increases the export of carbon into the deep ocean via sinking. However, specific polysaccharides contributing to particle formation and carbon export remain unknown. Here, we studied microalgae polysaccharide composition in a system of reduced complexity consisting of lab grown monospecific cultures of the centric diatom species Thalassiosira weissflogii and Chaetoceros socialis. We followed the abundance and dynamics of five specific polysaccharide types in the dissolved and particulate organic matter (DOM and POM) for two weeks. Polysaccharides were detected using monoclonal antibodies (mAbs) specific for β-1,4-mannan, β-1,4-xylan, arabinogalactan, and two fucose-containing sulfated polysaccharide (FCSP) epitopes. Additionally, glycan composition of all samples was analyzed by monosaccharide analysis. The time series revealed polysaccharides partition differently between the dissolved and particulate carbon pools. β-1,4-xylan and β-1,4-mannan were mainly present in POM, possibly as cell wall polymers, while FCSPs were found in both DOM and POM. The data showed that the main glycan component secreted by diatoms was fucose-containing polysaccharide, which accumulated in DOM over time. Roller tank experiments were used to induce aggregate formation finding FCSP transitioned from DOM to POM under aggregating conditions. These results suggest that diatom-secreted FCSPs are involved in the formation of aggregates, which promote the formation of particles, and potentially carbon export.