The issues of the formation of the largest lakes in Europe - Ladoga and Onega are considered in the article. The main aim was to identify features of the basins development from their origin to modern condition. The newest geological and geophysical data obtained in 2014-2021 was used to achieve the goal. Both depressions, in which modern lake basins are located, were formed in the Late Proterozoic. In the Late Quaternary, the glacier significantly modeled the pre-Quaternary relief. Glacial tongues significantly expanded the negative forms of the pre-glacial relief. At the same time, the glacier also formed positive landforms, such as moraines and esker ridges. Such ridges intersect the Lake Ladoga center and mark the position of the Neva stage. Structural features of the supraglacial section are considered in detail. It is shown that in both lakes the structure of the upglacial section is approximately the same and is associated with the gradual retreat of the glacier from the lake basins. Thus, it is shown that, despite the similarity of the main stages of paleogeographic development, each lake basin was characterized by its own features and their development itself occurred asynchronously.