AbstractEnvironmental conditions, physiology and community composition of phytoplankton and the carbon and nitrogen isotope signature (δ13CPOC and δ15NPN) of particulate organic matter (POM) often covary across marine environments. However, little was known on the link of δ13CPOC and δ15NPN and the community and biochemical composition of phytoplankton. In this study, particulate organic carbon (POC) and nitrogen (PN), δ13CPOC, δ15NPN, phytoplankton community composition and biomass were determined during summer, along with environmental variables, in the shelf of the northern South China Sea influenced by the Pearl River plume, upwelling and anticyclonic eddy. Our results show that variability in δ13CPOC and δ15NPN along an environmental gradient is coupled with shifts in phytoplankton community composition and carbon to chlorophyll a (C:Chl a) ratio of phytoplankton. Low δ13CPOC values (−28.4 to −27.0‰) at nearshore stations (salinity <21) were primarily due to terrestrial POM input. High δ13CPOC (>−21.0‰) and δ15NPN (>5.6‰) values are most likely attributed to high abundance of diatoms induced by riverine nutrients in the plume‐impacted waters with intermediate salinity (21< salinity <33). Low δ13CPOC (<−22.0‰) and δ15NPN (−1.1–3.7‰) values are associated with high abundance of slow‐growing cyanobacteria in the oligotrophic area (salinity >33), where the lowest δ15NPN is most likely attributed to high abundance of N2‐fixing Trichodesmium spp., due to the influence of the anticyclonic eddy. Therefore, hydrodynamics modulates the biochemical composition and community composition of phytoplankton, leading to changes in δ13CPOC and δ15NPN. Our findings advance our understanding of the coupling of physical and biogeochemical processes in marginal seas.