Due to their large extent and high primary productivity, tropical dry forests (TDF) are important contributors to atmospheric carbon exchanges in subtropical and tropical regions. In northwest Mexico, a bimodal precipitation regime that includes winter precipitation derived from Pacific storms and summer precipitation from the North American monsoon (NAM) couples water availability with ecosystem processes. We investigated the net ecosystem production of a TDF ecosystem using a 4.5 year record of water and carbon fluxes obtained from the eddy covariance method complemented with remotely sensed data. We identified a large CO2 efflux at the start of the summer season that is strongly related to the preceding winter precipitation and greenness. Since this CO2 efflux occurs prior to vegetation green-up, we infer that respiration is mainly due to decomposition of soil organic matter accumulated from the prior growing season. Overall, ecosystem respiration has an important effect on the net ecosystem production but can be overwhelmed by the strength of the primary productivity during the NAM. Precipitation characteristics during NAM have significant controls on sustaining carbon fixation in the TDF into the fall season. We identified that a threshold of ~350 to 400 mm of monsoon precipitation leads to a switch in the annual carbon balance in the TDF ecosystem from a net source (+102 g C/m2/yr) to a net sink (−249 g C/m2/yr). This monsoonal precipitation threshold is typically exceeded one out of every 2 years. The close coupling of winter and summer periods with respect to carbon fluxes suggests that the annual carbon balance is dependent on precipitation amounts in both seasons in TDF ecosystems.