Purpose <p><i>Suaeda salsa</i> (<i>S. salsa</i>) is widely distributed in coastal salt marshes and contains phytolith-occluded carbon (PhytOC) with stability on a millennium scale. Vegetation coverage in these salt marshes fluctuates with variances in estuarine channel migrations; however, studies on the relationships between carbon sequestration and estuarine channel migrations are lacking. This study aims to investigate the relationship between river flow variability and changes in the carbon sequestration potential of <i>S. salsa</i>.</p> Methods <p><i>S. salsa</i> and soils in the Yellow River Delta (YRD) were sampled in July 2022. The relationships between phytolith/PhytOC content in <i>S. salsa</i> and environmental factors in soils were analyzed.</p> Results <p>The phytolith and PhytOC contents in <i>S. salsa</i> were 27.71 ± 9.11 and 1.72 ± 2.13&#xa0;g kg^− 1, respectively. The phytolith content was positively correlated with the water content in soil, and the PhytOC content was negatively correlated with the organic carbon content in soil. The annual amount of PhytOC in <i>S. salsa</i> sequestered 68.22—347.73 t hm^− 2 of CO₂ from 1989 to 2020, with variations that coincided with periods of water flow and river channel change.</p> Conclusions <p>The carbon sequestration potential through PhytOC of <i>S. salsa</i> may be enhanced by increasing soil moisture and managing organic matter content.</p>