Mangrove forests are among the most productive ecosystems in the world. These tropical and subtropical coastal forests provide a wide array of ecosystem services, including the ability to sequester and store large amounts of ‘blue carbon’. Given rising concerns over anthropogenic carbon dioxide (CO2) emissions, mangrove forests have been increasingly recognized for their potential in climate change mitigation programs. However, their productivity differs considerably across environments, making it difficult to estimate carbon sequestration potentials at regional scales. Additionally, most research has focused in humid and tropical latitudes, with limited studies in arid and semi-arid regions. A semi-arid mangrove forest in Magdalena Bay, Baja California Sur, Mexico was studied to quantify the average net ecosystem exchange (NEE), determine the annual carbon (C) budget and the environmental controls driving those fluxes. Measurements were taken during 2012-2013 using the eddy covariance technique, with a daily mean NEE of -2.25 +/- 0.4 g C m-2 d-1 and annual carbon uptake of 894 g C m-2 y-1. Daily variations in NEE were primarily regulated by light, but air temperature and vapor pressure deficit were strong seasonal drivers. Our research demonstrates that despite the harsh and arid climate, the mangroves of Magdalena Bay were nearly as productive as mangroves found in tropical and subtropical climates. These results broaden understanding of the ecosystem services of one of the largest mangrove ecosystems in the Baja California peninsula, and highlight the potential role of arid mangrove ecosystems for C accounting, management and mitigation plans for the region.