Characterising available habitat cover in wetlands is an important task that has applications over multiple research and management areas. Obtaining such information is difficult when required over large areas or for historical time periods. The Greater Melbourne Region includes over 69,000 waterbodies. To help inform Melbourne Water’s management of these waterbodies, we aimed to characterise changes in the extents of water, vegetation and bare ground in waterbodies across the landscape over a period from 1986 to 2020. To do this, we built models of cover types using satellite data. Here we discuss our modelling process, showcase some of the applications arising from our work, and highlight some of the pitfalls we came across along the way.