Small lakes and their sediments are widely used for palaeolimnological reconstructions. Often only one core from the deepest part of the lake is used for reconstructing the lake catchment development, water-level changes and climate. To interpret palaeoinformation correctly, it is necessary to understand the spatio-temporal dynamics and the essence of lake basin evolution (topography, sedimentation zones, etc.) during the selected time period. The current study focuses on reconstructing the development of Lake V ike Juusa (southern Estonia) during the Holocene with the help of 3D digital elevation models compiled for the palaeolake stages at 9000 BP, 8000 BP, 4000 BP, 2000 BP and the present. The results suggest that we have to consider lake stages as completely different lakes with different sedimentation patterns – the hypsocraphic curve of Lake V ike Juusa was convex at the beginning of the Holocene and is concave nowadays. The proportion of the accumulation areas varied from 6% to 60% at the beginning of the Holocene and is around 30% nowadays. In order to understand lake basin development and water-level changes, the sampling sites should be selected close to the transitional zone and more than one core from a lake is needed. Commonly the sites located spatially rather close to each other have significantly different sedimentation patterns. Three-dimensional digital elevation models of palaeolake basins are useful tools for visualizing data and for hypothesizing about possible effects of lake-level fluctuations on the lake and its sedimentation regime.