Water pollution in China is severe and combined pollution with multiple stressors poses a great challenge to watershed risk management. Under the conditions of combined pollution, recognizing high-risk areas of concern, identifying key toxicants from multiple stressors and comprehensively assessing their ecological risk are the urgent and difficult tasks in watershed management. Traditional ecological risk assessment mainly focuses on single pollutant, which is difficult to obtain holistic information on the risk related to combined pollution. Based on the current research progress of combined pollution assessment, this review proposes a framework for ecological risk assessment of combined pollution in watersheds, including recognition of high-risk areas, identification of key toxicants and comprehensive assessment of ecological risk of the key toxicants. Firstly, high-risk areas are identified by weight of evidence analysis, which integrates information from both laboratory and in situ exposure and effect analyses. Most of exposure and effect data so far are based on chemical analyses and bioassays in the laboratories, yet bias may exist in extrapolating information from laboratory data to the field. Alternatively, in situ analysis serves an effective approach in reducing this extrapolation bias and, at the same time, more realistically recording biological effects under some field exposure scenarios, such as pulse exposure. Passive sampling devices have been applied for in situ exposure assessment. The integration of passive sampling with in situ organism exposure chambers successfully gains both chemical and toxicological lines of evidence for ecological risk assessment. Secondly, key toxicants in the high-risk areas are identified using toxicity identification evaluation (TIE) and effect-directed analysis (EDA) techniques. Conventional TIE is of environmental relevance by using whole organism bioassays; however, it is lack of effective methods in identifying major contributors to the toxicity because it merely focuses on analyzing the contaminants in target lists. Alternatively, EDA is a powerful tool in identifying key organic toxicants with a combination of chemical fractionation and analysis of targeted and non-targeted contaminants. Nevertheless, the common use of in vitro bioassays and exhaustive extraction make EDA lack of environmental relevance. Therefore, integrating TIE and EDA would provide an environmentally relevant method to effectively determine causality of sediment toxicity by combining the merits of the two methodologies. To improve the accuracy of toxicity identification, bioavailable extraction and dosing techniques are recommended to be incorporated into the integrated method. Thirdly, probabilistic ecological risk of the key toxicants in the high-risk areas is evaluated using tiered ecological risk assessment methods. Hazard quotient method has been widely used in providing conservative risk screening information, but uncertainties could not be quantified with this method. Therefore, a probabilistic assessment method, including distributions of exposure, response and hazard quotient levels, is proposed to achieve a holistic ecological risk assessment. At the end, recent developments and challenges in ecological risk assessment of combined pollution in watersheds are prospected. Overall, integrating the understanding of joint toxicity mechanisms in combined pollution risk assessment, improving the ability in non-targeted analysis and developing bioavailability-based sediment thresholds are important to assess ecological risk of combined pollution in watersheds.