A periphyton-based index for biological integrity was developed to assess the ecological status of lakes and reservoirs in Baiyangdian Watershed, China. Periphyton and environmental surveys were conducted at 20 sites during 2009-2010. A total of 22 surveyed metrics of periphyton, which were classified into 6 categories: biomass groups, community structure, pigment ratios, bacteria diversity, enzyme activities, and metabolism were evaluated in order to understand their responsiveness to environmental degradation. Out of these 22 metrics, six metrics were selected to constitute the periphyton-based index for biological integrity: chlorophyll b, chlorophyll c: chlorophyll a ratio, alkaline phosphatase activity, bacteria dominance, net daily metabolism, and autotrophic index by sensitivity and redundancy analysis. Then the periphyton-based index for biological integrity was verified by an independent validation-site data set. The test results indicated the index could not only discriminate disturbed sites from reference sites, but also be triggered by land use types. The scores of periphyton-based index for biological integrity were significantly correlated with the environmental parameters, especially ammonia nitrogen and total phosphorus. These results suggest that this index may be a potential tool for assessing the ecological status of lakes and reservoirs, polluted mainly by organic contaminants in Baiyangdian Watershed.