Carbon cycling in rivers and estuaries is of critical importance to their management. The Hawkesbury-Nepean is an iconic Australian river system, providing drinking water to over 4 million people in Sydney and the surrounding region in New South Wales. Over the course of the region’s development, water quality in the river system has been degraded and shifts in the river’s biogeochemistry have been observed. With increasing development in the area, it is critical to gain a better understanding of the carbon sources, sinks, and transformations within the system and their broader implications. Here, we have collected one of the most comprehensive carbon budgets developed for any estuary, with 18 fifty-hour time series measurements of organic carbon (DOC, TOC), inorganic carbon (TA, DIC) and greenhouse gases (pCO2 and pCH4). Our study encompasses an 80 km section of the river, from freshwater, through the tidal freshwater zone and into the estuary over distinctly different hydrological conditions. This work identifies key processes driving carbon transformations and greenhouse gas emissions. Overall, this work characterises the major carbon fluxes in the Hawkesbury-Nepean catchment and their drivers, which will influence management in the region as development increases.