To prevent the loss of biodiversity in northern Central America, which is one of 34 global biodiversity hotspots, the Mesoamerican Biological Corridor, a network of protected parks and reserves has been proposed. While on-going deforestation to croplands and pastures outside the protected regions is likely to effect the dry season precipitation over the regenerated and extant forests in the proposed protected regions, global climate change driven precipitation changes may also be a significant factor, at least at some locations. This study compares the effects of land cover change to the effects of elevated greenhouse gas concentrations on precipitation in the proposed areas of the Mesoamerican Biological Corridor network. Using 5 consecutive dry season simulations of the effects of land cover change that included dry, wet and normal years, and using statistically downscaled global climate model (GCM) precipitation from the fourth assessment report (AR4), a larger expanse of the proposed protected regions was found more sensitive to precipitation decreases due to land cover changes. Two specific protected regions however stand out: the Maya Highlands and some areas of the Maya lowlands that were more sensitive to global climate change driven precipitation decreases. In these protected regions it is likely that irrespective of local policies the climate change signal would dominate.