Understanding broad trends in the distribution and composition of wetlands is essential for making evidence-based management decisions. Determining temporal change in the extent of inundation in wetlands using remote sensing remains challenging and requires on-ground verification to determine accuracy and precision. Therefore, optimization and validation of remote sensing methods in threatened wetlands is a high priority for their conservation. Despite their ecological importance in the landscape, we have little knowledge of the variation in the spatial extent of inundation in upland lagoons, a threatened ecological community in New South Wales, Australia. Our project developed locally trained algorithms to predict the extent of water and emergent vegetation using imagery from the Landsat-5, -7, and -8 satellites. The best model for upland lagoons used shortwave infrared reflectance (performing better than normalized difference spectral indices), with model accuracy against validation transects greater than 95%. We applied the model to images from 1988 to 2020 across 58 lagoons to generate a dataset that demonstrates the variable water regime and vegetation change in response to local rainfall over 32 years such as in the lagoons. Our results reduce threats to a dynamic threatened ecological community by filling an important knowledge gap and demonstrate a valuable method to understand historical and current changes in the hydrology of dynamic wetland systems more broadly.