Since 2005, Morocco has designated many Ramsar wetlands, yet little is known about factors determining their occupation by waterbird communities. In this study, we assessed the relationship between the occupation of Moroccan Ramsar wetlands during the breeding season by two globally threatened waterbirds, the marbled teal Marmaronetta angustirostris and the ferruginous duck Aythya nyroca, and geographical, topographical and macrohabitat factors. Habitat-based statistical models showed that the presence of these two threatened waterfowl species at Moroccan wetlands was positively correlated with the number of emergent vegetation species, and negatively correlated with altitude and the distance to the nearest coastline. These results highlighted previous findings regarding the significant and positive relationship between the number of plant taxa and the number of threatened waterbird species at Moroccan wetlands. Further investigations should be conducted at regional (Maghreb region) and international (Mediterranean area) levels (i) to allow a global analysis and benchmarking between regions, (ii) to improve the provision of information to support sound management interventions, and (iii) to contribute to conservation management planning for these threatened waterfowl species.