Changes in wetland environments can alter the dynamics of waterbird populations. We investigated the effects of hydrological and landscape variables on the abundance of resident waterbirds (ducks, fish-eaters, large waders, small waders, and vegetation gleaners) from 2003 to 2014 in Bung Boraphet, Thailand's largest freshwater wetland. Generalized linear mixed models were used to determine the effects of environmental variables on waterbird numbers, and generalized additive mixed models were used to identify the threshold for each effect. The results revealed that the population of all waterbirds declined by 27% from 2003 to 2014 with highest decline of 56% in ducks. Increasing water depth was negatively correlated with the abundance of small waders and vegetation gleaners. Higher concentrations of dissolved oxygen in the water increased the abundance of fish-eaters, while marshy areas were positively associated with the abundance of ducks, large waders, and vegetation gleaners. The abundance of fish-eaters, large waders, and small waders were negatively associated with the spatial area of waterbodies. Expanding human settlements decreased the abundance of vegetation gleaners, while vegetation infested by Mimosa pigra decreased the abundance of large waders. The study concludes that the maintenance of an optimal water depth and quality, preservation of critical marsh habitats, eradication of invasive species, and restrictions on new human settlements adjacent to wetlands are all necessary to conserve resident waterbird populations. Validating these findings in additional research sites is recommended before applying it to a broader landscape level.