Estuaries with extensive salt marshes play an important role in storing and moving carbon in coastal areas. In this study, we used water quality sensors and computer models to track how dissolved organic carbon (DOC) moves in and out of the Plum Island Estuary in Massachusetts. We found that the timing and strength of water flow, strongly affect carbon movement. Delay in the water draining from marshes also affects when and how much carbon is moved. Our results show that understanding both water flow and drainage timing is essential for predicting how estuaries contribute to the movement of carbon in coastal zones.