Algal organic matter (AOM), produced by marine phytoplankton during bloom periods, may adversely affect the performance of membrane processes in seawater desalination. The polysaccharide fraction of AOM has been related to (bio)fouling in micro-filtration and ultrafiltration, and reverse osmosis membranes. However, so far, the chemical structure of the polysaccharides released by bloom-forming algae is not well understood. In this study, dissolved fraction of AOM produced by three algal species (Chaetoceros affinis, Nitzschia epithemoides and Hymenomonas spp.) was characterized using liquid chromatography–organic carbon detection (LC-OCD) and fluorescence spectroscopy. Chemical structure of polysaccharides isolated from the AOM solutions at stationary phase was analyzed using proton nuclear magnetic resonance (H-NMR). The results showed that production and composition of dissolved AOM varied depending on algal species and their growth stage. AOM was mainly composed of biopolymers (BP; i.e., polysaccharides and proteins [PN]), but some refractory substances were also present.H-NMR spectra confirmed the predominance of carbohydrates in all samples. Furthermore, similar fingerprints were observed for polysaccharides of two diatom species, which differed considerably from that of coccolithophores. Based on the findings of this study,H-NMR could be used as a method for analyzing chemical profiles of algal polysaccharides to enhance the understanding of their impact on membrane fouling.