Submerged macrophytes play an important role beyond that of primary production, as they provide increased structural complexity and niche potentials for fish. However, most of the scientific attention on habitat use in fish and the influence of macrophytes have been given to small and shallow lakes, where the vegetated areas are well-developed and the availability of a large deep water refugium is absent or limited. Our goal was to gain a detailed understanding of the structuring effect the submerged macrophytes have on fish communities in deep lakes. In order to achieve this, we contrasted two newly formed deep lakes of similar size and colonization history, but one with and the other without submerged macrophytes. We used the latest developments in high-resolution positioning telemetry to assess individual habitat use and activity patterns in the different species of the multispecies assemblages in the two lakes – Lake Most and Lake Milada.