Aim Assessing long-term (1992–2009) trends of littoral invertebrate and phytoplankton metacommunities in boreal lakes with emphasis on separating the nestedness and turnover components of beta diversity. Deriving implications for regional biodiversity conservation and management, based on a data-intensive approach with high ecological realism. Location Sweden (Northern Europe). Methods A recently published method was used to partition beta diversity into species turnover and nestedness components. Regression analyses were used to test for monotonic temporal change of these diversity fractions through time. Associations between the temporal diversity patterns of taxonomic groups and environmental variables were studied using correlation analyses. Results Turnover of both metacommunities increased monotonically over the study period, while nestedness decreased. In invertebrates, these changes correlated mainly with regional changes in acidity, while phytoplankton responded more to changing water clarity. Nestedness and turnover patterns were inversely correlated in both groups, but neither turnover nor nestedness was correlated between invertebrates and phytoplankton. Nestedness of both groups explained a lower percentage of the partitioned variance compared with turnover. Main conclusion Results suggest that all lakes contribute more equally to regional diversity over time and are, as a result, all potential targets of management actions. Not only is a regional conservation strategy logistically difficult, it is also a financially expensive expectation.