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Global measures of biodiversity indicate consistent decline, but trends reported for local communities are more varied. Therefore, we need better understanding of mechanisms that drive changes in diversity of local communities and of differences in temporal trends between components of local diversity, such as species richness and species turnover rate. Freshwater ecosystems are vulnerable to multiple stressors, and severe impacts on their biodiversity have been documented. We studied species richness and composition of local boreal waterbird communities in 1990/1991 and 2016 at 58 lakes distributed over six regions in Finland and Sweden. The study lakes represented not only local trophic gradients but also a latitudinal gradient in the boreal biome. While species richness tended to be lower in 2016 than in 1990/1991, species turnover was relatively high. Within foraging guilds, local species richness of diving ducks and surface feeding waterbirds decreased, whereas that of large herbivores increased. The number of species gained in local communities was higher in lakes with rich vegetation than in lakes with sparse vegetation. Conservation of boreal freshwater ecosystems would benefit from recognizing that large-scale environmental changes can affect local diversity via processes operating at finer scales.