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There are physical, chemical, and biological methods to control algae, and their efficiency requires evaluation. In the field, monitoring and evaluating the overall algal concentration is challenging due to factors such as the flow rate, inhomogeneous distribution of algae in the water body, and limitations in the number of samples for microscopic analysis. In this study, we analyzed total and cyanobacterial chlorophyll a (Chl-a) using a FluoroProbe sensor and microscopic data collected from March to November 2019. The Pearson correlation coefficient of log(x + 1) values revealed a significant positive correlation between four harmful cyanobacteria and cyanobacterial Chl-a (r = 0.618, p < 0.01). Furthermore, we explored the potential of evaluating the efficiency of algal control using sensors by acquiring three-dimensional, spatially continuous data for an algal fence, a physical algae control technology installed at the Daecheong Dam in 2021. The results confirmed that sensors can effectively evaluate algal control technology. This study demonstrates the effectiveness of using sensors to assess the efficiency of physical algal control.