The objective of this database is to measure and identify the seasonal variation of meteorological conditions and atmospheric carbon flux of a semi-arid mangrove ecosystem on the coastal line of Magdalena Bay in the Mexican State of Baja California Sur. This dataset is part of a larger project entitled Carbon Flux in a Semi-Arid Mangrove Ecosystem in Magdalena Bay, B.C.S Mexico. The project and meteorological station were managed and operated primarily by the first author. Local support was provided by the Centro de Investigaciones Biológicas del Noroeste (CIBNOR) and funded by San Diego State University and NOAA Educational Partnership Program/ Center for Earth System Sciences and Remote Sensing Technologies.------------------The study site is located along the northern extent of Magdalena Bay (Bahia Magdalena), which is about 10 km north of the fishing town of Puerto Adolfo Lopez Mateos, BCS, Mexico (25°15'44N, 112° 4'48W). The area is a contiguous series of productive and biologically diverse embayments, intertidal mud flats, and mangrove-lined canals bounded by islands and sand bars that extend for 175 km along the Pacific coast of BCS. The site is located within the largest of these bays in the northwest region of Magdalena Bay in an area bordered by the sandy barrier island of Isla Magdalena, which forms a protected inner shelf lagoon that connects the inner lagoons and canals to the Pacific Ocean via the "Boca de Soledad". Magdalena Bay is characterized by a high floral and faunal diversity, where the arid desert region transitions into a coastal area. Seasonal upwelling in the sub-tropical California Current allows high rates of productivity in the bay, which is dominated by surf grass, eel grass, intertidal mud flats, salt marshes, and mangrove lined coastlines. The dominant mangroves species found in this area are red (Rhizophora mangle), white (Laguncularia racemosa) and black (Avicennia germinans) mangrove trees.------------------Data was collected for 22 days between January 8 and 30, 2012; for 69 days during summer between June 20 and August 28th, 2012; and for 19 days between January 5 and 24 in 2013. January 2012, and January 2013 were grouped together as winter and the months of June through August were grouped as Summer for seasonal period analysis.Meteorological variables were averaged over 30-minute intervals from measurements taken every 10 seconds and stored using a datalogger (CR3000, Campbell Scientific Inc.) with a removable 2 GB compact flash memory card: Air temperature (Tair), and relative humidity (RH), (HMP45c, Vaisala, Helsinki, Finland) were measured at 4.5 m in a radiation shield. Vapor pressure deficit (VPD) was calculated from air temperature and relative humidity. Incoming photosynthetic active radiation (PAR) was measured by a quantum sensor (LI-190 SB, LI-COR, Lincoln, NE, USA) at 4m above the ground. Net radiation (Rn) (Q-7.1, REBS Inc., Seattle, WA, USA) was measured within the upwind sampling area at 4 m above the ground. Ground heat flux, G, (HFT3, REBS Inc., Seattle, WA, USA) was measured at a depth of 5cm below the ground surface, and copper-constantan thermocouples were placed at depths of 2, 5, and 10cm below the surface to measure soil temperature.