The Aral Sea has shrunk drastically over the past 50 years, largely due to water abstraction from the Amu Darya and Syr Darya rivers for land irrigation. Over a longer timescale, Holocene palaeolimnological reconstruction of variability in water levels of the Aral Sea since 11,700 BP indicates a long history of alternating phases of regression and transgression, which have been attributed variously to climate, tectonic and anthropogenic forcing. The hydrological history of the Aral Sea has been investigated by application of a variety of scientific approaches, including archaeology, palaeolimnological palaeoclimate reconstruction, geophysics, sedimentology, and more recently, space science. Many issues concerning lake level variability over the Holocene and more recent timescales, and the processes that drive the changes, are still a matter for active debate. Our aim in this article is to review the current debates regarding key issues surrounding the causes and magnitude of Aral Sea level variability on a variety of timescales from months to thousands of years. Many researchers have shown that the main driving force of Aral Sea regressions and transgressions is climate change, while other authors have argued that anthropogenic forcing is the main cause of Aral Sea water level variations over the Holocene. Particular emphasis is made on contributions from satellite remote sensing data in order to improve our understanding of the influence of groundwater on the current hydrological water budget of the Aral Sea since 2005. Over this period of time, water balance computation has been performed and has shown that the underground water inflow to the Aral Sea is close to zero with an uncertainty of 3 km3/year.