A two years study was carried out in two reaches of meta-hyporhithal zone of rivers in the Dyje River Basin (Morava - Danube Catchment), Czech Republic. The reaches are without recent regulation and with normal background of euthrophization. Typical habitats (patches) as riffle with gravel bars, cobbles and boulders, riffle with gravel bars and woody debris, pools with gavel bottom, pools with gravel and cobble bottom, riparian zones - gravel, moody, woody debris and high plants were selected. The patches were very variable in space and time, so we evaluated especially changes in the area of cross section profile, substrate of bottom, current in the bed layer and discharge on defined profile. Function and ecological importance of these dynamic patches will be evaluated according meiobenthic (algae, protozoa and crustaceans) and macrozoobentic assemblages. Spatial and temporal differences showed function of habitats in compliance with patch dynamic concept.