Pterins function as pigments, cofactors, precursors, and redox sensors in bacteria, playing roles in detoxification, global nutrient cycles, and unconventional carbon and nitrogen utilization. This talk focused on the biogeochemical characteristics in the Jiulong River Estuary and Xiamen Bay, analyzing the spatiotemporal distribution of sediment microbial pterins in estuarine wetland during dry and flood seasons. We explored the biological significance of pterins based on correlations between environmental factors and biological indices, offering new insights into estuarine ecological processes. Our findings show that during the flood season, the primary source of microbial pterins is phytoplankton, including freshwater algae and cyanobacteria, due to high productivity from upstream inputs. In contrast, heterotrophic contributions to microbial pterins increase during the dry season and in reducing sediment environments. Sediments with reducing conditions yield more dihydro-neopterin and neopterin, while biopterin and its metabolite, isoxanthopterin, are more easily retained in water. These results clarify the distribution, sources, and migration processes of microbial pterins in nearshore waters and estuarine sediments. Furthermore, the strong correlation between Chl-a and pterins suggests that microbial pterin bioavailability may enhance phytoplankton growth, indicating that increased pterin levels could signal marine algal blooms. However, this proliferation accelerates the consumption of microbial pterins, making pterin levels a potential indicator for marine algal blooms. In addition, sediment C/N and isoxanthopterin levels imply coastal carbon sink capacity indirectly, necessitating further study to investigate carbon sinks with pterin biomarkers application in the ocean.