Phosphorus (P) is an important substance for growth of phytoplankton and an efficient index to assess water quality. However, estimation of TP concentration in waters by remote sensing must be associated with optical substances like chlorophyll-a (Chla) and suspended particulate matter (SPM). Based on the good correlation between the suspended inorganic matter (SPIM) and P in Lake Hongze, we used the direct and indirect derivation methods to develop algorithms for total phosphorus (TP) estimation with MODIS/Aqua data. Result demonstrates the direct derivation algorithm based on 645 nm and 1240 nm of MODIS/Aqua performs a satisfied accuracy (R2 = 0.75, RMSE = 0.029mg/L, MRE=39% for training dataset, R2 = 0.68, RMSE = 0.033mg/L, MRE=47% for validate dataset), which is better than that of indirect derivation algorithm. 645 nm and 1240 nm of MODIS/Aqua are the main characteristic band of SPM, so that algorithm can effectively reflect P variations in Lake Hongze. Additionally, the ratio of TP to SPM is also positively correlated with the accuracy of the algorithm as well. The proportion of SPIM in SPM has a complex effect on the accuracy of the algorithm. When SPIM accounts for 78%, the algorithm achieves the highest accuracy. Furthermore, the performance of this direct derivation algorithm was examined in two inland lakes in China (Lake Nanyi and Lake Chaohu), it derived the expected P distribution in Lake Nanyi whereas the algorithm failed in the Lake Chaohu. Different water properties influence significantly the accuracy of this direct derivation algorithm, while TP, Chla and suspended particular inorganic matter (SPOM) of Lake Chaohu are much higher than those of the other two lakes, thus it is difficult to estimate TP concentration by simple band combination in Lake Chaohu. Although the algorithm depends on the dataset used in development, it usually presents a good estimation for those waters where SPIM dominated, especially when SPIM accounts for 60% to 80% of SPM. This research proposed an direct derivation algorithm for the TP estimation for turbid lake and will provide a thereotical and practical references for extending optical remote sensing application and the TP empirical algorithm of Lake Hongze help for the local government management water quality.