Introduction: The Florida Everglades has undergone significant ecological change spanning the continuum of disturbance to restoration. While the restoration effort is not complete and the ecosystem continues to experience short duration perturbations, a better understanding of long-term C dynamics of the Everglades is needed to facilitate new restoration efforts. This study evaluated temporal trends of different aquatic carbon (C) pools of the northern Everglades Protection Area over a 20-year period to gauge historic C cycling patterns. Dissolved inorganic C (DIC), dissolved organic C (DOC), particulate organic C (POC), and surface water carbon dioxide (pCO 2(aq) ) were investigated between May 1, 1994 and April 30, 2015. Results: Annual mean concentrations of DIC, DOC, POC, and pCO 2(aq) significantly decreased through time or remained constant across the Water Conservation Areas (WCAs). Overall, the magnitude of the different C pools in the water column significantly differed between regions. Outgassing of CO 2 was dynamic across the Everglades ranging from 420 to 2001 kg CO 2 year −1 . Overall, the historic trend in CO 2 flux from the marsh declined across our study area while pCO 2(aq) largely remained somewhat constant with the exception of Water Conservation Area 2 which experienced significant declines in pCO 2(aq) . Particulate OC concentrations were consistent between WCAs, but a significantly decreasing trend in annual POC concentrations was observed. Conclusions: Hydrologic condition and nutrient inputs significantly influenced the balance, speciation, and flux of C pools across WCAs suggesting a subsidy-stress response in C dynamics relative to landscape scale responses in nutrient availability. The interplay between nutrient inputs and hydrologic condition exert a driving force on the balance between DIC and DOC production via the metabolism of organic matter which forms the base of the aquatic food web. Along the restoration trajectory as water quality and hydrology continues to improve, it is expected that C pools will respond accordingly.