Saltpans converted into protected areas form key habitats for breeding and migrating waterbirds. Their abiotic variations are mainly controlled by site managers, offering near-experimental templates for the study of coastal ecosystem dynamics. The present study aims to estimate the effects of hydraulic and physico-chimical variations of water conditions in saltpans on the taxonomic diversity of waterbirds, on a study site located on the French Mediterranean shore (salins d’Hyères, Var). We quantified the species richness, total abundance and Pielou’s equitability of the local bird assemblage from standardized decadal bird counts from 2013 to 2016. We subsequently regressed these indices against measurements of water level, salinity and oxygen concentration. Our results show temporal variations in bird diversity that differ among functional guilds and match with fluctuations in resource and habitat availability. They reveal patterns of complementarity in site use within the study area. Overall, our results describe a pattern of multiscale community dynamics which could contribute to orient site management towards an ecosystem approach, accounting for regional processes and species’ ecological functions.