The carbon dioxide flux through the air-water interface of coastal estuarine systems must be quantified to understand the regional balance of carbon and its transport through adjacent coastal regions. We estimated and calculated the emissions of carbon dioxide (FCO₂) and the partial pressure of CO₂ (pCO₂) values in 28 estuarine environments at a variety of spatial scales in the northern and northeastern regions of Brazil. The results showed a mean FCO₂ (water to air) of 55 ± 45 mmol·m(-2)·d(-1). Additionally, a negative correlation between dissolved oxygen saturation and pCO₂ was observed, indicating a control by biological processes and especially by organic matter degradation. This leads to increased dissolved CO₂ concentration in estuarine waters which results in a pCO₂ that reached 8,638 μatm. Our study suggests that northern and northeastern Brazilian estuaries act as sources of atmospheric CO₂. The range of pCO₂ observed were similar to those found in inner estuaries in other places around the world, with the exception of a few semi-arid estuaries (Köppen climate classification - BSh) in which record low levels of pCO₂ have been detected.