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Many wetlands around the world that occur at the base of watersheds are under threat from land‐use change, hydrological alteration, nutrient pollution, and invasive species. A relevant measure of whether the ecological character of these ecosystems has changed is the species diversity of wetland‐dependent waterbirds, especially those of conservation value. Here, we evaluate the potential mechanisms controlling variability over time and space in avian species diversity of the wetlands in the Palo Verde National Park, a Ramsar Site of international importance in Costa Rica. To do so, we assessed the relative importance of several key wetland condition metrics (i.e., surface water depth, wetland extent, and vegetation greenness), and temporal fluctuations in these metrics, in predicting the abundance of five waterbirds of high conservation value as well as overall waterbird diversity over a 9‐yr period. Generalized additive models revealed that mean NDVI, an indicator of vegetation greenness, combined with a metric used to evaluate temporal fluctuations in the wetland extent best predicted four of the five waterbird species of high conservation value as well as overall waterbird species richness and diversity. Black‐bellied Whistling‐ducks, which account for over one‐half of all waterbird individuals, and all waterbird species together were better predicted by including surface water depth along with wetland extent and its fluctuations. Our calibrated species distribution model confidently quantified monthly averages of the predicted total waterbird abundances in seven of the 10 sub‐wetlands making up the Ramsar Site and confirmed that the biophysical diversity of this entire wetland system is important to supporting waterbird populations both as a seasonal refuge and more permanently. This work further suggests that optimizing the timing and location of ongoing efforts to reduce invasive vegetation cover may be key to avian conservation by increasing waterbird habitat.