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Multiple bio-optical measurements of optically active substances were conducted in Taihu Lake, Chaohu Lake, Three Gorges Reservoir, and Dianchi Lake (China). A hierarchical cluster analysis was applied to remote sensing spectra (Rrs(λ)), by which those waters were clustered into three optically distinct types (Type I, Type II, and Type III). Absorption coefficients of phytoplankton were simulated using the linear function and the coefficients of the functions varied in different water types. The slope of colored dissolved organic matter (CDOM) absorption could be clustered into two classes, one class of high slope for Types I and II, whereas the other class of low slope for Type III. A uniform model was used for parameterization of the nonalgal particles absorption coefficients spectral between different water types. The power-law function was used to parameterize the scattering coefficient and the slope of scattering spectra could be classified into two groups of high slope for Types I and II, low slope for Type III. The composition of particles, particulate scattering, and nonalgal particulate absorption are the factors controlling the variability in Rrs(λ) for corresponding type waters. Those results support such a fact that it is indispensable to classify waters before developing a model to estimate water quality parameters for multi-type optical waters.