Widespread across northern permafrost landscapes, thermokarst ponds and lakes provide vital wildlife habitat and play a key role in biogeochemical processes. Stored in the sediments of these typically shallow and dynamic waterbodies are rich sources of paleoenvironmental information whose potential has not yet been fully exploited, likely because of concerns over stratigraphic preservation and challenges to develop reliable sediment core chronologies. Here, we present an overview of recently-derived informative paleolimnological reconstructions based on multi-parameter analysis of sediment archives from permafrost aquatic basins. We include examples from across the Canadian North, Alaska, and Siberia that illustrate their value for providing insights into temporal patterns of lake inception, catchment erosion, aquatic productivity, hydrological evolution, and landscape disturbances. Although not captured in our survey, emerging research directions focused on carbon accumulation, storage, and balance hold much promise for contributing to global climate change science.