Stream is the basic component unit of terrestrial water environment and their ecological conditions are important for sustainable functions in natural systems. For the development of a sustainable river system the ecological conditions were investigated along Huaijiuhe River near Beijing, which is part of the water conservation district of Huairou Reservoir. For the ecological assessment a Channel-Wetland-Riparian Index (CWRI) were applied. The index compares the natural conditions of the investigated stream to be reference sites, and evaluates the near-natural degree of structure and functions of degraded stream ecosystems which is disturbed by human activities or sudden natural changes. CWRI is based on twenty-two quantitative indicators and thirteen qualitative indicators including ecological, hydrological and geographical aspects. The majority of quantitative indicators are represented by ratios in order to avoid the problems with the variety of stream ecosystem. The near-natural degrees of stream ecosystems can be classified into four grades: (Ⅰ) natural grade (no human disturbance); (Ⅱ) near-natural grade (minimal artificial disturbance); (Ⅲ) semi-degraded grade (serious artificial disturbance); (Ⅳ) complete degraded by human activities. Investigations were carried out at seventeen reaches to have a maximum number of replicates. The assessment results are easily affected by the random of field investigations, existing fuzziness and probability, therefore, taking the fuzzy probability assessment method to construct this assessment system.