Lake sediments constitute natural archives of past environmental changes. Historically, research has focused mainly on generating regional climate records, but records of human impacts caused by land use and exploitation of freshwater resources are now attracting scientific and management interests. Long-term environmental records are useful to establish ecosystem reference conditions, enabling comparisons with current environments and potentially allowing future trajectories to be more tightly constrained. Here we review the timing and onset of human disturbance in and around inland water ecosystems as revealed through sedimentary archives from around the world. Palaeolimnology provides access to a wealth of information reflecting early human activities and their corresponding aquatic ecological shifts. First human impacts on aquatic systems and their watersheds are highly variable in time and space. Landscape disturbance often constitutes the first anthropogenic signal in palaeolimnological records. While the effects of humans at the landscape level are relatively easily demonstrated, the earliest signals of human-induced changes in the structure and functioning of aquatic ecosystems need very careful investigation using multiple proxies. Additional studies will improve our understanding of linkages between human settlements, their exploitation of land and water resources, and the downstream effects on continental waters.