Phosphorus (P) is an important substance for the growth of phytoplankton and an efficient index to assess the water quality. However, estimation of the TP concentration in waters by remote sensing must be associated with optical substances such as the chlorophyll-a (Chla) and the 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 the total phosphorus (TP) estimation with the MODIS/Aqua data. Results demonstrate that the direct derivation algorithm based on 645 nm and 1240 nm of the MODIS/Aqua performs a satisfied accuracy (R2 = 0.75, RMSE = 0.029mg/L, MRE = 39% for the training dataset, R2 = 0.68, RMSE = 0.033mg/L, MRE = 47% for the validate dataset), which is better than that of the indirect derivation algorithm. The 645 nm and 1240 nm of MODIS are the main characteristic band of the SPM, so that algorithm can effectively reflect the P variations in Lake Hongze. Additionally, the ratio of the TP to the SPM is positively correlated with the accuracy of the algorithm as well. The proportion of the SPIM in the SPM has a complex effect on the accuracy of the algorithm. When the 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 Lake Chaohu. Different water properties influence significantly the accuracy of this direct derivation algorithm, while the 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 the TP concentration by a simple band combination in Lake Chaohu. Although the algorithm depends on the dataset used in the development, it usually presents a good estimation for those waters where the SPIM dominated, especially when the SPIM accounts for 60% to 80% of the SPM. This research proposed a direct derivation algorithm for the TP estimation for the turbid lake and will provide a theoretical and practical reference for extending the optical remote sensing application and the TP empirical algorithm of Lake Hongze’s help for the local government management water quality.