Abstract The dynamics of lateral nutrient fluxes through hydrological movements are crucial for understanding ecological functions related to the flow of energy, materials, and organisms across various spatiotemporal scales. To investigate the connectivity of multiple spatial flow processes, we conducted a one-year field study to measure lateral hydrologic carbon (C) and nitrogen (N) fluxes across the continental shelf in the Yangtze estuary. We observed a significant correlation between the differences in remote sensing-based estimates of gross primary production (GPP) (ΔGPPMODIS) and the differences in eddy covariance (EC) tower-based GPP (ΔGPPEC) at both high-elevation and low-elevation sites. Our findings indicate that the saltmarsh acts as a net source of dissolved total C while serving as a net sink for dissolved total N. Furthermore, there was a significant correlation in the total dissolved stoichiometry of the C/N ratio between imports from and exports to adjacent aquatic systems. These findings highlight the importance of integrating ecological stoichiometric principles to improve our understanding of the complex relationships among physical, chemical, and ecological processes, particularly within the context of the meta-ecosystem framework. Additionally, when reciprocal hydrological lateral C and N flows are considered, a single ecosystem can function as both a source and sink within the meta-ecosystem framework.