The spatial distribution of avifauna was documented in Magdalena Bay, the largest coastal wetland on the Pacific coast of the Baja California peninsula. An inventory of waterbirds in the three wetland zones of Magdalena Bay-Almejas, Baja California Sur was conducted by boat. Composition, abundance, and distribution of species were determined in 12 coastal censuses conducted from February 2002 to February 2003. A total of 207,383 individuals of 80 species and 20 families were recorded. Seven listed species breed in the wetland. Only ten out of 80 species were very common, while the others were occasional along the coastline. Guilds with highest populations were pelicans and allies (54%), followed by shorebirds (23%), and gulls, terns and skimmers (14%). The highest richness of 63 species was recorded in the Santo Domingo Channel in autumn. In contrast, the highest abundance (50,082) was recorded in fall in Magdalena Bay. Migratory birds explained spatial and temporal changes in richness, while resident pelicans and allies explain abundance variations. The highest species richness was observed in mangrove zones, particularly in the Santo Domingo Channel. Therefore, this habitat together with breeding and gathering places used for other activities, should be primary targets for future management and conservation initiatives.