Aquaculture offers a major opportunity for the economic development of Baja California Sur (BCS), Mexico. The severely limited freshwater supply and the geographic isolation of the state place limits on other productive activities. Despite the aridity, the natural vegetation of BCS is diverse and structurally complex with a high percentage (20%) of endemic species. In this work we compare the environmental impacts produced by two kinds of aquaculture systems: coastal ponds vs. inland ponds. Construction and operation of coastal ponds does not require destruction of the natural vegetation and, as is true for inland ponds. Coastal ponds are also compatible with conservation of mangroves, sea grasses and sensitive habitats for fish and mollusks. To reduce the negative impacts of aquaculture and to protect the vegetation of Baja California Sur, we recommend the use of coastal ponds for shrimp production.