Using various communities as indicators of the biotic integrity of waters has been developed. However, compared to other organisms, such as fish or macroinvertebrates, there are few studies in lakes/reservoirs using phytoplankton as an indicator. Taking a Chinese reservoir as an example, an evaluation method with reference to phytoplankton index of biotic integrity was developed to assess the ecological status of the reservoir. In the method, a factor analysis was used to reduce the metric sets regarding phytoplankton and to identify a potentially lower number of unobserved/imaginary variables to represent the characteristics of the community. The kind of phytoplankton index was calculated by determining the corresponding factor scores for each site. The results showed that four factors can be indicative of ecological integrity and provide a monitoring tool. The relations between the factors and water quality parameters also indicated that the factors could reflect the water quality status. The scores can truly reflect the changes in water quality, and each factor representing the different characteristics of a phytoplankton community revealed changes in water quality from different views. This study was an important trial for the development of a biological index based on phytoplankton in a lake/reservoir without reference sites and presented a simple and practical approach for assessing the status of waters. The methods based on factor analysis for creating a phytoplankton index of biotic integrity can be recommended for determining the ecosystem health of waters.