Flow regime characteristics (magnitude, frequency, duration, seasonal timing and rates of change) play a primary role in regulating the biodiversity and ecological processes in rivers. River classification provides the foundation for comparing the hydrologic regimes of rivers and development of hydro-ecological relationships to inform environmental flow management and river restoration. This paper presents a classification of natural flow regimes and hydrologic changes due to dams and floodgates in the Huai River Basin, China, in preparation for an environmental flow assessment. The monthly natural flow regime of 45 stations in the upper and middle Huai River Basin were simulated for the period 1963–2000, based on the hydrological model SWAT (Soil and Water Assessment Tool). Six classes of flow patterns (low or high discharge, stable or variable, perennial or intermittent, predictable or unpredictable) were identified based on 80 hydrologic metrics, analysed by hierarchical clustering algorithms. The ecologically relevant climatic and geographic characteristics of these flow classes were tested for concordance with, and to strengthen, the hydro-ecological classification. The regulation of natural flow patterns by dams and floodgates changed flows at some locations within each flow class and caused some gauges to shift into another class. The research reported here is expected to provide a foundation for development of hydro-ecological relationships and environmental flow methods for wider use in China, as well as setting a new scientific direction for integrated river basin management in the Huai River Basin. Copyright © 2011 John Wiley & Sons, Ltd.