Using as a model system a long-term data set (1984–2014) of waterbird counts at nine large wetlands of Eastern Spain (Comunidad Valenciana), we explored the ecological drivers of population fluctuations, both during the wintering (34 species) and breeding (36 species) seasons. Most species showed increasing trends (80% during breeding, 62% in winter), including both initially common and rare species, suggesting a positive effect of site protection policies that were mainly applied in the 1980s. Specialised freshwater species such as diving ducks and coots did not show population recovery, most probably due to the characteristic tendency of shallow lagoons to remain eutrophic even after several decades of the implementation of sewage management and water purification. In fact re-introduction of a diet-specialist (red-knobbed coot) failed but that of a diet-generalist (purple swamphen) succeeded. Waterfowl hunting and the abandonment of rural practices also probably played a role in the lack of recovery by some species. Population trends of breeding species were more dependent on local conditions than trends of wintering populations. Body size could also have some influence on growth rates because some of the smallest species of shorebirds and Laridae (such as Kentish plovers, little terns and black-headed gulls) showed decreasing trends in one or both seasons. Finally, a few species were gained for the system as new wintering species, probably due to climate warming. Our results suggest that growth rates alone are poor descriptors of population fluctuations, especially for birds and other vagile taxa, and that it is more appropriate to interpret trends when considering natural regions spatially, and when growth rates are analysed within the time scale of the theoretical logistic curve.