Aquatic ecosystem health is often defined in terms of an earlier ‘preferred’ state described by earlier observations or palaeolimnology. Many tropical lakes are deteriorating, but few have a known history. Lake Naivasha (Kenya) however may be unique in having a 30000-year palaeoecological history during which it has undergone major fluctuations. It has a written history beginning in the 19th century, and has since experienced extreme changes through drought and human activity. It is now a Ramsar site, and so provides an ideal case study to examine the meaning of ‘aquatic health’. Although it has periodically dried, in its ‘natural’ state the lake supported dense submerged and fringing vegetation, much of which has now been lost. It is moderately eutrophic, has an unbalanced water budget and has experienced a number of exotic species introductions. The history of scientific work at Lake Naivasha is summarised from the earliest expedition in 1929, and with palaeolimnological evidence, is used to chart changes in the lake system including its chemistry, phytoplankton, macrophytes, macroinvertebrates and vertebrates. As the lake shows broad natural fluctuations, no single ‘natural’ state can be described. Despite anthropogenic impacts, the lake can still be considered reasonably ‘healthy’ although many of its components have been changed by human activity. Ongoing pressures on the system give cause for concern about its future condition and management.