In the past few years problems concerning both flood protection and aquatic ecology have increased markedly in most rivers of the Bohemian Massif, mostly due to a special type of ‘fine sediment’ stress. Excessive loads of coarse sand or fine gravel, respectively, caused by various anthropogenic impacts, have lead to deposits that affect both the local flooding situation and the ecological conditions of entire river reaches. Mobile substrate layers fill up coarse sediments and even pools with consequences for the habitat suitability of the interstices.