In the master’s thesis we discuss the influence of different types of substrate and morphological changes of riverbed on the stream velocity structure. The emphasis is on velocity measurements close to the riverbed, where the most of water organisms, especially macroinvertebrates, actually live. The measurements of flow velocities above different substrates in the Glinšcica stream, carried out in the summer 2010, are presented. The instrument used for velocity measurements was acoustic Doppler velocimeter FlowTracker Handheld ADV. In the results, we compare vertical velocity profiles across the river cross-section, the velocity profiles above different natural substrates or above the concrete channel and the velocity profiles at the same point at different water stages. We also compare turbulent kinetic energy density on morphologically different stream reaches. Furthermore, we estimate the influence of biocenosis on water velocities and vice versa.