Field experiments were conducted on Lake Taihu in November 2008 and April 2009,and on Lake Chaohu in June 2009. The water remote sensing reflectance was analyzed by factor analysis method. Furthermore, Chlorophyll and total suspended matter concentration were inversed using different factors of remote sensing reflectance, and universality of inverted factor was veri-fled too. Chlorophyll concentration of Lake Taihu in spring was inversed by the first factor, and relative error and root-mean-square error are 22.1% and 3.48g/L, respectively. However, this method failed in inversing of autumn of Lake Taihu and Lake Chaohu.Concentration of total suspended matter was inversed by the second factor, and relative error and root-mean-square error were 13.9% and 11.33 mg/L, respectively. This method was suitable in Lake Chaohu and autumn of Lake Taihu. Applicability of the first factor of remote sensing reflectance to inverse chlorophyll concentration was limited, and applicability of the second factor of remote sensing reflectance to total suspended matter concentration was certain universal.