The observation of the phytoplankton distribution with a high spatiotemporal resolution is necessary to track the nutrient sources that cause algal blooms and to understand their behavior in response to hydraulic phenomena. Photography from UAVs, which has an excellent temporal and spatial resolution, is an effective method to obtain water quality information comprehensively. In this study, we attempted to develop a method for estimating the chlorophyll concentration from aerial images using machine learning that considers brightness correction based on insolation and the spatial distribution of turbidity evaluated by satellite image analysis. The reflectance of harmful algae bloom (HAB) was different from that of phytoplankton seen under normal conditions; so, the images containing HAB were the causes of error in the estimation of the chlorophyll concentration. First, the images when the bloom occurred were extracted by the discrimination with machine learning. Then, the other images were used for the regression of the concentration. Finally, the coefficient of determination between the estimated chlorophyll concentration when no bloom occurred by the image analysis and the observed value reached 0.84. The proposed method enables the detailed depiction of the spatial distribution of the chlorophyll concentration, which contributes to the improvement in water quality management in reservoirs.