The dynamics of hydrological lateral nutrient fluxes contribute to our understanding of ecological functions related to energy, materials, and organism flows across various spatiotemporal scales. To explore the connectivity between multiple spatial flow processes, we conducted a one-year field measurement to assess lateral hydrologic carbon (C) and nitrogen (N) fluxes over 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) (∆GPPMODIS) and the differences in eddy covariance (EC) tower-based GPP (∆GPPEC) at both high-elevation and low-elevation sites. Over the course of a year, our predicted daily maximum tidal elevation (TE) closely matched the observed values in the creek, which facilitated the development of theoretical models to simulate biogeochemical cycling processes and aquatic ecosystem functions. Our findings indicate that the studied saltmarsh acts as a net exporter of dissolved total C (DTC) while serving as a net sink for dissolved total N (DTN). Furthermore, there is a significant correlation in the total dissolved stoichiometry of the C/N ratio between imports and exports. These findings highlight the importance of integrating ecological stoichiometric principles to gain a deeper understanding of the complex relationships between physical, chemical, and biological processes, particularly within the context of the meta-ecosystem framework. Additionally, when considering reciprocal hydrological lateral C and N flows, single ecosystem can function both as sources and sinks within the meta-ecosystem framework.