Monitoring inundation in flow-dependent floodplain wetlands is important for understanding the outcomes of environmental water deliveries that aim to inundate different floodplain wetland vegetation types. The most effective way to monitor inundation across large landscapes is with remote sensing. Spectral water indices are often used to detect water in the landscape, but there are challenges in using them to map inundation within the complex vegetated floodplain wetlands. The current method used for monitoring inundation in the large floodplain wetlands that are targets for environmental water delivery in the New South Wales portion of the Murray–Darling Basin (MDB) in eastern Australia considers the complex mixing of water with vegetation and soil, but it is a time-consuming process focused on individual wetlands. In this study, we developed the automated inundation monitoring (AIM) method to enable an efficient process to map inundation in floodplain wetlands with a focus on the lower Lachlan floodplain utilising 25 Sentinel-2 image dates spanning from 2019 to 2023. A local adaptive thresholding (ATH) approach of a suite of spectral indices combined with best available DEM and a cropping layer were integrated into the AIM method. The resulting AIM maps were validated against high-resolution drone images, and vertical and oblique aerial images. Although instances of omission and commission errors were identified in dense vegetation and narrow creek lines, the AIM method showcased high mapping accuracy with overall accuracy of 0.8 measured. The AIM method could be adapted to other MDB wetlands that would further support the inundation monitoring across the basin.