Pterins are essential biomolecules widely conserved in diverse microbes. First discovered as enzymatic cofactors, pterins participate in countless enzymatic reactions such as photoreceptor signal transduction and redox. Pterins are involved in light energy capture and UV protection as pigments as well. In this study, pterins were widely distributed in microorganisms in the Jiulong River Estuary and nearshore seawaters, but the abundance and composition of microorganisms in different habitats determine the difference in the concentration of pterins. Estuarine sediments tend to conserve reduced DNP and biosynthetic precursor NP but are more likely to retain BP and final product IP in the waterbody. Microbial pterins in the summer (Flood season: 0.23-136 pM) were significantly higher than in the autumn (Dry season: 0.92-16.9 pM). Aqueous microbial pterins were related to plankton abundance and have favorable coupling with chlorophyll a (Chl-a), indicating higher productivity of estuarine diatoms driven by estuarine nutrients and particulate organic carbon inputs facilitated the higher concentration of pterins. In summer, photoautotrophic phytoplankton was the major sources of pterins; while the proportion of heterotrophic prokaryotes contributing to pterins have increased in autumn with low productivity. In comparison, sediment pterins were about three orders of magnitude higher than in the seawaters, and the reduced form DNP (44-60.8 nM) in the sediment was 3-10 times that of other pterins. There was no significant difference in the distribution of pterins between seasons, mainly due to the decomposition of bacteria in the sediment, implying biodegradation was an important supplementary source of pterins. Therefore, microbial pterin molecules have the potential to be biomarkers for revealing marine biogeochemical cycles and primary production processes.