Abstract. Biological diversity is inextricably linked to community stability and ecosystem functioning, but our understanding of these relationships in freshwater ecosystems are largely based on short-term observational, experimental, and modelling approaches. Using a multidecadal diatom record for the past 15,800 years from Lake Baikal, we investigate how three ecosystem components – diversity, productivity, and stability – have responded to climate changes on long-timescales. In addition, we investigate how the relationships between diversity, productivity and stability have changed through time in response to these changes. We show that abrupt changes in diatom stability and diversity during the late glacial and early Holocene are part of a network of responses across southern Siberia as a result of extrinsically-forced climate instability. Productivity – diversity relationships were strongly coupled during the late glacial, which we suggest is linked to resource availability, but showed little relationship during the Holocene, perhaps due to few resources being limiting for extended periods of time. For example, periods of low diatom diversity are associated with peak palaeoproductivity, and coincide with climate disturbance events. Such strong negative relationships may reflect resources becoming limiting during palaeoproductivity, leading to monospecific diatom blooms. While species fluctuations respond rapidly to changing resources during much of the Holocene, the ecosystem function of primary production appears to be relatively resilient. Our study provides important perspectives on lake community stability and ecosystem function in relation to rapid periods of climate change.