Hydro peaking causes an important environmental impact on running water ecosystems. Many affected rivers have a poor ecological status. In rivers affected by hydro peaking, the flow conditions are highly complex and difficult to grasp. To develop a general framework for detecting and characterizing sub-daily flow fluctuations, we analysed more than 500 Austrian hydrographs, covering the whole range from unimpacted to heavily impacted rivers. Different fluctuation types could be identified according to the potential source: e.g. sub-daily flow fluctuations caused by hydro peaking, rainfall or snow and glacier melt. Additionally, the term ‘hydro fibrillation’ was established, to indicate frequently occurring artificial fluctuations with comparably low intensities. An automatic procedure was used to detect frequency and intensity of each flow fluctuation. Using variables based on duration curves of flow fluctuation rates (ramping rates), amplitudes, flow ratios, durations and daily numbers of fluctuations, a predictive model (linear discriminant analysis) was fitted to classify hydrographs into predominant fluctuation regimes. This is the basis for a detailed investigation of present sub-daily flow regimes and to analyse the differences between the regimes. Based on the results, we finally propose a general framework that enables a standardized assessment of flow fluctuations regarding event intensities and/or event timing. The proposed framework offers a standardized selection of particular flow fluctuations referring to increase and decrease events separately. The selection of specific flow fluctuations can be defined with respect to several research questions (e.g. ecologically relevant fluctuations), which offers a wide range of applications. Copyright © 2015 John Wiley & Sons, Ltd.