Aquatic plants and lake bottoms in optically shallow waters (OSWs) wield great influence on reflectance spectra, resulting in the inapplicability of most existing bio-optical models for water colour remote sensing in lakes. Based on radiative transfer theory and measured spectra from a campaign for Lake Taihu in October 2008, absorption and backscattering coefficients were used to simulate the remote-sensing reflectance, which are considered to be reliable if matched to their measured counterparts. Several cases of measured spectra at different depths, Secchi disk depth transparency, and aquatic plant height and coverage were analyzed thoroughly for spectral properties. The contribution of aquatic plants was evaluated and compared with the measured and simulated remote-sensing reflectance values. This is helpful for removing the influence of aquatic plants and lake bottoms from the spectra and for constructing an improved chlorophyll a retrieval model for OSWs, such as that for Lake Taihu, China.