Coastal vegetated ecosystems are major organic carbon (OC) and total nitrogen (TN) sinks, but the mechanisms that regulate their spatial variability need to be better understood. Here we assessed how superficial sedimentary OC and TN within intertidal vegetated assemblages (saltmarsh and seagrass) vary along a flow gradient, which is a major driver of sediment grain size, and thus of organic matter (OM) content. A significant relationship between flow current velocity and OC and TN stocks in the seagrass was found, but not in the saltmarsh. OC and TN stocks of the saltmarsh were larger than the seagrass, even though that habitat experiences shorter hydroperiods. Mixing models revealed that OM sources also varied along the flow gradient within the seagrass, but not in the saltmarsh, showing increasing contributions of microphytobenthos (17–32%) and decreasing contributions of POM (45–35%). As well, OM sources varied vertically as microphytobenthos contribution was highest at the higher intertidal saltmarsh (48%), but not POM (39%). Macroalgae, seagrass and saltmarsh showed low contributions. Local trade-offs between flow current velocities, hydroperiod and structural complexity of vegetation must be considered, at both horizontal and vertical (elevation) spatial dimensions, for better estimates of blue carbon and nitrogen in coastal ecosystems.