Waterbird surveys following the annual African Waterbird Census were conducted in the Antsalova region of western Madagascar from 2002 to 2004. Seven wetland sites were monitored: five freshwater lakes, one alkaline lake and one marsh. Three of the five fresh water lakes were in the Manambolomaty Lakes Complex, a RAMSAR site. A total of 37,836 individual birds were recorded belonging to 55 species representing 15 families. The marsh had the highest waterbird abundance of all sites with an average of 3,616.3 ± 461 individuals (N = 3 years). Species diversity index was highest in the freshwater lakes with an average of 2.53 ± 0.07, and the lowest was recorded at Antsohale Lake with an average of 2.22 ± 0.08. The waterbird abundance varied significantly between freshwater lakes and the marsh from 2002 to 2004, between freshwater lakes and the alkaline lake in 2003 and 2004, and between the alkaline lake and marsh. The net difference in species abundance between the Manambolomaty Lakes Complex and the other lakes varied significantly. In contrast, species richness between the Manambolomaty Lakes Complex and the other lakes did not vary. Several threatened species were at population levels observed ten years earlier.