A significant disagreement between the expected (modelled) and the observed average cohort lengths of littoral dwelling juvenile burbot (Lota lota L.) was observed in Lake Constance, Germany. From September of their first year (age-0), particularly the largest members of the cohort were under-represented in littoral habitats but over-represented in the profundal zone. This indicates a size-selective inter-habitat migration, with autumnal lake level drawdown as the major proximate factor. The study shows that water level fluctuations affect not only the behaviour and distribution of individual fish within the littoral itself but can also control the temporal and spatial distribution patterns of a particular fish species in an entire lake ecosystem.