Coastal pond-to-mangrove restoration has become a prominent Nature-based Solution, yet its short-term ecological effects on waterbird communities remain unclear. We assessed taxonomic, functional, and compositional responses of waterbirds to large-scale restoration in Bamen Bay, Hainan Island, using BACI-style comparisons between restored and unrestored aquaculture ponds in 2021 and 2023. Restored areas exhibited higher taxonomic α diversity and functional richness (p < 0.001), coinciding with rapid habitat diversification following hydrological reconnection. Species richness (p < 0.001), Shannon diversity (p < 0.01), and functional richness (p < 0.01) were consistently higher in restored areas than in aquaculture ponds. In contrast, β diversity patterns diverged between habitats: restored areas remained relatively stable, whereas aquaculture ponds showed greater between-year compositional change (p < 0.05). Guild-specific responses revealed contrasting patterns: herons showed higher diversity in restored habitats (p < 0.05), whereas shorebirds exhibited no significant changes (p > 0.05), consistent with their dependence on open mudflats that were only partially retained. Although no significant declines were detected, functional richness tended to be lower in 2023 (p > 0.05), and ongoing mudflat loss suggests potential long-term risks for mudflat specialists, warranting extended monitoring. Taken together, our findings suggest that effective pond-to-mangrove restoration in Bamen Bay should balance mangrove expansion with the retention of tidal flats and managed shallow-water habitats to support diverse waterbird assemblages.