There are more than 123 coastal lagoons in the Mexican coastal zone covering an approximate area of 12,555 km². The length of these lagoons represents between 30 % and 35 % of the 11,543 km of the Mexican coast. Magdalena Bay, Mexico, is the largest bay in the Baja California peninsule (Fig. 1). The Bay is a lagoon system with three main areas, the northernmost called Laguna Santo Domingo, the central part Magdalena Bay, and the southernmost Almejas Bay. The lagoon system has a total length of 250 km, covering an area of 2,200 km² that includes 1,453 km² of the lagoon basin and 747 km² of mangrove forest, sand dunes, and wetlands (Malagrino, 2007). Currently Magdalena Bay is very important for the economy of the state of Baja California Sur, 50 % of the artisan fisheries activities are established in this zone. To avoid conflicts between environmental conditions and commercial productive activities we studied and summarized the main biological, physical, chemical and socioeconomic aspects of Magdalena Bay, in order to determine where, and how, new clam culture projects must be established. Aquaculture world production has maintained a sustained growth in several countries for the last 15 years, generating both positive and negative impacts, on social (Bayle, 1988; Primavera, 1991; Lebel et al., 2002), economic (Kautsky et al., 1997), and natural systems (Páez-Osuna, 2001; Macintosh, 1996). Mexico, being no exception, has developed these activities at similar rates going from 0 tons in 1984, to more than 62,000 tons in 2003 (SAGARPA-CONAPESCA, 2003). Moreover, it is expected that aquaculture activities will increase explosively in the coming years. If aquaculture activities flourish, as it is foreseen in this region, there will be direct conflicts with artisan fishing activities, ecotourism and tourist activities foreseen to be carried out in the region, and with the conservation of the environment, including sand dunes and mangrove fragile ecosystems.