With the expansion in urbanization, understanding how biodiversity responds to the altered landscape becomes a major concern. Most studies focus on habitat effects on biodiversity, yet much less attention has been paid to surrounding landscape matrices and their joint effects.

We investigated how habitat and landscape matrices affect waterbird diversity across scales in the Yangtze River Floodplain, a typical area with high biodiversity and severe human-wildlife conflict.

The compositional and structural features of the landscape were calculated at fine and coarse scales. The ordinary least squares regression model was adopted, following a test showing no significant spatial autocorrelation in the spatial lag and spatial error models, to estimate the relationship between landscape metrics and waterbird diversity.

Well-connected grassland and shrub surrounded by isolated and regular-shaped developed area maintained higher waterbird diversity at fine scales. Regular-shaped developed area and cropland, irregular-shaped forest, and aggregated distribution of wetland and shrub positively affected waterbird diversity at coarse scales.

Habitat and landscape matrices jointly affected waterbird diversity. Regular-shaped developed area facilitated higher waterbird diversity and showed the most pronounced effect at coarse scales. The conservation efforts should not only focus on habitat quality and capacity, but also habitat connectivity and complexity when formulating development plans. We suggest planners minimize the expansion of the developed area into critical habitats and leave buffers to maintain habitat connectivity and shape complexity to reduce the disturbance to birds. Our findings provide important insights and practical measures to protect biodiversity in human-dominated landscapes.