Both climate change and local anthropogenic pressures have impacted biogeochemical cycling in coastal systems. Here we study a coastal ecosystem in North Carolina in order to determine spatial relations, seasonal changes, and overall fluxes of carbon, as well as the influences of these factors on the biogeochemistry of the system as a whole. Partial pressure of carbon dioxide (pCO2), percent dissolved oxygen (DO%), total dissolved inorganic carbon (DIC), total alkalinity (TA), carbon isotopes of dissolved inorganic carbon, and pH values—amongst additional data—were collected from numerous study locations in the Cape Lookout region of North Carolina in April 2017, October 2017, April 2018, June 2018, and October 2018. Three creeks flowing into Jarrett Bay depict distinct seasonal trends of varying levels of pCO2 and DO% related to phytoplankton cycles. Most notably, the salt marsh ecosystem surrounding Smyrna Creek causes particularly high pCO2 levels in this creek, peaking at 14606 µatm in the head of the creek in June 2018. However, creeks were occasionally undersaturated in pCO2, likely from phytoplankton blooms occurring during spring and summer. Carbon flux from these three creeks into Jarrett Bay is evident, as is further flux of CO2 through the sound and out into the ocean where the CO2-saturated estuarine waters combine with the less CO2-rich marine waters to produce ocean values of ~625 µatm. TA shows an increasing spatial trend moving through the system with the lowest values (1.109–2.002 mmol kg-1) in the creeks and Jarrett Bay, and the highest values (2.320–2.342 mmol kg-1) in the ocean. DIC also increases from Jarrett Bay (1739–1774 µmol kg-1) to the ocean (1927–1966 µmol kg-1); however, the head of Smyrna Creek exhibits notably high DIC values of ~2074 µmol kg-1. This reveals that CO2 is the main contributor to DIC within the salt marsh. Similarly, TA increases moving from Smyrna Creek out through the system into the ocean because CO2 does not contribute to TA while HCO3- does. Plotting DIC against TA indicates that inorganic carbon likely originates from a combination of sulfate reduction, aerobic respiration, and CO2 degassing. Calculations of CO2 flux indicate that the estuarine system as a whole (including the small marsh creeks that flow into the bay) is a source of CO2 to the atmosphere with an average air–sea flux of 70.2 mmol m-2 day-1.