Based on the bio-optical properties of water constitute in the Taihu, Chaohu, Dianchi lake and Sanxia reservoir, bio-optical retrieval model for the suspended particle matter and chlorophyll-a were established according to the radiance transfer model and genetic optimization algorithm. The measured data in situ was used to test this optimized model. The results indicate that, the model can remove the influence of noise on the final retrieval precision in a certain degree. The retrieval precision of this model in the Taihu, Chaohu, Dianchi lake and Sanxia reservoir is different due to the variation of suspended particle matter and chlorophyll-a bio-optical properties. However, in general, this model can retrieve the concentration of suspended particle matter and chlorophyll-a with a preferable precision. Two parameters, mean absolutely percentage error (MAPE) and root mean square error (RMSE) which represent the retrieval precision of suspended particle matter, can reach to a value of 23% and 15.13mg/L, respectively (the number of sampling points is 228). The retrieval precision of chlorophyll-a (MAPE and RMSE) can reach to 26% and 17.68μg/L, respectively with the same number of sampling points.