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Since 2005, Morocco has designated 28 Important Bird Areas (IBA) and Ramsar wetlands for waterbirds, yet little is known about how waterbird communities are changing over time and space, within and between sites. We assessed the relationships between species numbers of overall breeding waterbirds, as well as those of Anatidae, Rallidae and Podicipedidae, and geographical, topographical and macrohabitat factors. Species richness of overall waterbirds and Anatidae were positively correlated with: (i) extent of emergent vegetation, (ii) number of plant species present, and (iii) altitude. Species richness of Rallidae was positively correlated with: (i) latitude, and (ii) different beds of emergent vegetation, while that of Podicipedidae was exclusively correlated with altitude. These results suggest that breeding waterfowl are significantly related to habitat characteristics, most importantly vegetation structure, and altitude. Our findings give support to the idea that large mountain wetlands protected areas provide valuable habitat to breeding waterbirds in this region, by providing larger buffer zones with fewer human activities, such as hunting, urbanization and tourism disturbance. This study provides a platform from which we can advance the scientific research on Moroccan IBA and Ramsar wetlands.