This work was aimed at comparing the instream flow environment of four basic hydromorphological units of a mountain gravel-bed river: pools, runs, riffles and rapids. A survey was performed during the average flow stage on the Skawa River in southern Poland. In the 3.5 km long reach, 31 physical habitats were surveyed: eight pools, eight runs, nine riffles and seven rapids. Using Micro ADV Sontek equipment, instantaneous velocity time series components were measured at eight locations in three positions—z/h = 0.2, 0.4 and 0.6—in each unit. Turbulence descriptors—the mean components of velocity, turbulence intensities calculated as the root mean square of velocity component time series, turbulent kinetic energy TKE, Reynolds shear stresses and standard hydraulic attribute, i.e., Froude number—were estimated. Although there was a wide dispersion of the turbulence variable distributions, a standard tendency of decreased mean velocity and increased turbulence towards the bottom was observed. Most turbulence parameters—streamwise velocity, turbulence intensities, TKE and streamwise-vertical Reynolds shear stresses—reveal differences of instream flow environment between the pools, runs and riffles. In addition, the mean turbulence intensities suggested a 1:2:3:3 proportion of turbulence intensity in pools, runs, riffles and rapids, respectively. Riffles and rapids, in general, have similar turbulence values, whereas rapids are deeper and visually more energetic.