Boreal lakes undergo broad-scale environmental change over time, but biodiversity responses to these changes, particularly at macroecological scales, are not well known. We studied long-term trends (1992-2009) of environmental variables and assessed α, β, and γ diversity responses of phytoplankton and littoral invertebrates to these changes. Diversity was assessed based on taxon richness ("richness") and the exponentiated Shannon entropy ("diversity"). Almost all environmental variables underwent significant monotonic change over time, indicating mainly decreasing acidification, water clarity and nutrient concentrations in the lakes. These variables explained about 54 and 38% of variance in regression models of invertebrates and phytoplankton, respectively. Despite this, most diversity-related variables fluctuated around a long-term mean. Only α and γ richness and diversity of invertebrates increased monotonically through time, and these patterns correlated significantly with local and regional abundances. Results suggest that biodiversity in boreal lakes is currently stable, with no evidence of regional biotic homogenization or local diversity loss. Results also show that richness trends between phytoplankton and invertebrates were widely uncorrelated, and the same was found for diversity trends. Also, within each taxonomic group, temporal patterns of richness and diversity were largely uncorrelated with each other. From an applied perspective, this suggest that long-term trends of biodiversity in boreal lakes at a macroecological scale cannot be accurately assessed without multiple lines of evidence, i.e. through the use of multiple taxa and diversity-related variables in the analyses.