AbstractFST hemispheres of identical size but varying density were used to evaluate the intensity and duration of near‐bottom shear stresses during peaking hydropower floods of various magnitudes (maximum 345 m3s−1; baseflow 2.75 m3s−1). The FST values at single points were recorded at rapid intervals along previously surveyed transects during the rising limb of flood events at various distances from the hydropower facility. Whole transect evaluations were ‐accomplished after the ‘flood’ level had stabilized.Measurements of over 1300 FST values were significantly correlated with mean water column velocity and complex hydraulic conditions such as turbulence, shear velocity and viscous sublayer. FST hemispheres are a rapid means of characterizing hydraulic conditions in medium order rivers. Changes in near‐substrate hydraulic conditions were patchy and could be classified in terms of risk to fauna of either dislodgement or physical damage. Low risk (class 1) changes occurred when FST values increased rapidly but returned to initial values after a short period of time (<90 minutes) from the arrival of the peaking wave. Medium risk (class 2) changes occurred when FST values increased rapidly and decreased after a short period of time, but remained at levels higher than before the arrival of the flood wave. High risk (class 3) changes occurred when FST values increased rapidly and remained at high levels during the entire flood event.It is suggested that floods that do not initiate significant bed movement create a mosaic of patches of variable disturbance risk to benthic fauna. Rapid evaluation by FST hemispheres could be used to characterize the overall disturbance potential for the channel by the construction of a weighted index based on the frequency of the various risk classes occurring in the reach being evaluated. A more appropriate analysis of impacts of peaking hydropower and other flood events must include the existence of hydraulic refugia and the movement patterns of both benthic species and those species that occupy the