Global lake systems have been facing ubiquitous aquatic environmental challenges since 1950. The baseline and changing history of lake aquatic environments can be reconstructed by quantitative transfer functions, which aids in the assessment of the degree of human impact on lake ecosystems and in setting practical targets for ecological restoration. The basic processes of developing and applying quantitative transfer functions are first introduced. Then, typical case studies from various lake catchments are comprehensively summarized to elaborate on the application of quantitative transfer functions based on sedimentary subfossils to reconstruct lake aquatic environmental parameters. These parameters include water pH, total phosphorus, dissolved oxygen, transparency, water level, salinity, and temperature. The rate and magnitude of deviation from natural baselines due to anthropogenic disturbances, changing trajectories, and underlying mechanisms in typical lake environments in the Anthropocene were examined from multiple perspectives. Finally, constraints and prospects for lake transfer functions are discussed from the following aspects: developing new indicators and a multi-proxy approach, improving training sets with larger sample sizes and machine learning, improving modern ecological studies of biological indicators, and combining transfer functions with ecosystem modeling to further improve the quality of transfer functions and enlarge application fields to provide scientific references and guidance for future research.