The four largest Swedish lakes Vänern, Vättern, Mälaren and Hjälmaren all have a tectonic origin with multidirectional fault fissures, which influence the topography of the bottoms and the creation of subbasins. All the four lakes have been subject to several glacials, the latest of which started to recede from central Sweden c. 10 000 years ago. The many differences between the four lakes can be explained by their shapes, sizes and the relation between the sizes of the drainage basins and the size of the lakes. This paper focuses on processes considered relevant to aquatic organisms of the lakes: water balance, water residence time, water temperature, water exchange between subbasins within the lakes, and other internal water movements. Links between pollution, water exchange and retention of nutrients are discussed with an example from Lake Vänern.