Environmental conditions, physiology and community composition of phytoplankton and the carbon and nitrogen isotope signature (δC and δN) of particulate organic matter (POM) often covary across marine environments. However, little was known on the link of δC and δN and the community and biochemical composition of phytoplankton. In this study, particulate organic carbon (POC) and nitrogen (PN), δC, δN, 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 δC and δN along an environmental gradient is coupled with shifts in phytoplankton community composition and carbon to chlorophyll a (C:Chl a) ratio of phytoplankton. Low δC values (−28.4 to −27.0‰) at nearshore stations (salinity <21) were primarily due to terrestrial POM input. High δC (>−21.0‰) and δN (>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 δC (<−22.0‰) and δN (−1.1–3.7‰) values are associated with high abundance of slow-growing cyanobacteria in the oligotrophic area (salinity >33), where the lowest δN is most likely attributed to high abundance of N-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 δC and δN. Our findings advance our understanding of the coupling of physical and biogeochemical processes in marginal seas.