The human population is growing rapidly, increasing pressure on natural habitats. Suitable habitats for resident and migratory waterbirds are, therefore, more threatened. This study analyses how the presence of anthropogenic land cover (urban area and cropland) on multiple spatial scales affects the community composition of waterbirds along the Nile in Egypt. We analysed data collected during the international waterbird census, 2017-2018, combined with data from satellite images on land cover at a multi-spatial scale. The census covered 970 km, compromising 194 shoreline transects of 5 km along the River Nile, Egypt. The area includes a broad gradient of human disturbance, making this dataset ideal for assessing effects of anthropogenic land cover on waterbird community composition. We tested whether the waterbird community indices and guild composition were associated with urban area and cropland, and other land covers (e.g., grassland, wetland) at spatial scales of 100, 500, 1,000 and 5,000 m. We recorded over 96,000 waterbirds and show that landscape characteristics at larger spatial scales (5,000 m) explained more of the species and guilds’ presence than smaller scales. Species richness increased with increasing water surface area of the river within the transect and decreased with increasing urban area and cropland. Waders were negatively associated with urban area. Overall, the guilds’ composition was poorly predicted by anthropogenic land cover and other landscape compositions, probably because species within a guild do not react similarly to increasing human disturbance. The probability of observing red-listed species decreased with increasing urban area. With this study, we expand on the existing evidence by showing that species richness negatively correlates with anthropogenic pressure, and we highlight the importance of studying the responses of species rather than guilds. Our study shows the relevance of considering the landscape at larger scales while planning for conservation measures, especially in such human-dominated landscapes.