AbstractThe ability of communities to withstand stress or maintain their species composition over extended periods of environmental changes is a matter of major concern. Here, we utilize a dataset where microcrustacean communities were related to water chemistry in 82 boreal‐alpine lakes over a 50‐yr time span (1968 and 2016), with the same person involved in sampling both times ensuring identical sites and sampling protocols. Over this time span, there has been a 1–2°C increase in mean annual temperatures and prolonged growing seasons. Also, the strong changes in SO4 deposition and acidification, peaking in the early 1980s, followed by a recovery period, have caused not only an increase in pH but also a pronounced browning (elevated DOC) and reduced levels of Ca over the past three decades. Despite this, the microcrustacean diversity and community composition have remained remarkably stable, and this holds both for the species‐rich larger, boreal sites and the species‐poor alpine sites. While likely there are interannual fluctuations in species abundance, and perhaps species may also be missing for certain periods, a combination of local refugia, resting egg seed‐banks and a regional recolonization that may occur at the meta‐population level, aims at maintaining a strong stability in community composition.