We summarize the history of waterbird research in the Mediterranean region, how some of these activities developed into long-term ecological research programs, and how they created awareness of the need to conserve the species and their wetland habitats. We further analyze the impact of colonial waterbird studies on conservation actions and recommend how current research can be made relevant for conservation. An overview is presented of the development of midwinter counts and wetland site inventories, and the contribution of ecological studies to the conservation of colonial waterbirds and their habitats is summarized. There is still a lack of information on the distribution of the breeding colonies throughout the Mediterranean and of a coordinated population monitoring program. Data on feeding habitat and colony site requirements help to recognize those parts of the aquatic ecosystem that ought to be given conservation priority. The study of reproductive biology adds complementary data on the dependence of reproductive performance on environmental conditions. Ultimately, the identification of the environmental factors that influence population size is a key requirement for species conservation programs. This requires long-term studies. However, due to the infrastructure and long-term commitment involved, population studies expanding over decades have remained very few. To make the important investments in the study of colonial waterbird ecology more applicable to the conservation, management and restoration of their wetland habitats in the future, the collection of baseline monitoring data is required throughout the Mediterranean. Successfully tested ecological research methods need to be adopted in different parts of the Mediterranean and used in a coordinated way. Foraging ecology, ecotoxicology and the study of habitat requirements in relation to population dynamics are the research fields that can provide useful information for site-specific habitat management and restoration programs. Interdisciplinary projects between ecologists, hydraulic engineers, and land-use planners need to be developed. Finally, the results of the scientific studies need to be disseminated more widely, also in a form accessible to the administrator, political decision-maker, and local inhabitant of a wetland area.