Total phosphorus (TP) concentration is high in countless small inland waterbodies in Hubei province, middle China, which is threating the water environment. However, there are almost no ground-based water quality monitoring points in small inland waterbodies, because the cost of time, labor, and money is high and it does not meet the needs of spatiotemporal dynamic monitoring. Remote sensing provides an effective tool for TP concentration monitoring spatiotemporally. However, monitoring the TP concentration of small inland waterbodies is challenging for satellite remote sensing due to the inadequate spatial resolution. Recently, unmanned aerial vehicles (UAV) have been applied to quantitatively retrieve the spatiotemporal distribution of TP concentration without the challenges of cloud cover and atmospheric effects. Although state-of-the-art algorithms to retrieve TP concentration have been improved, specific models are only used for specific water quality parameters or regions, and there are no robust and reliable TP retrieval models for small inland waterbodies at this time. To address this issue, six machine learning methods optimized by intelligent optimization algorithms (IOA-ML models) have been developed to quantitatively retrieve TP concentration combined with the reflectance of original bands and selected band combinations of UAV multispectral images. We evaluated the performances of models in terms of coefficient of determination (R²), root mean squared error (RMSE), and residual prediction deviation (RPD). The results showed that the R² of the six IOA-ML models for training, validation, and test sets were 0.8856–0.984, 0.8054–0.8929, and 0.7462–0.9045, respectively, indicating the methods had high precision and transferability. The extreme gradient boosting optimized by genetic algorithm (GA-XGB) performed best, with the highest precision for the validation and test sets. The spatial distribution of TP concentration of each flight derived from different models had similar distribution characteristics. This paper provides a reference for promoting the intelligent and automatic level of water environment monitoring in small inland waterbodies.