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Algal blooms have been observed worldwide and have had a serious impact on industries that use water resources, which is a problem for people and the environment. For this reason, an algae warning system is used to count the number of cyanobacterial cells and the concentration of chlorophyll-<i>a</i>. Several studies using multispectral or hyperspectral data to estimate chlorophyll concentration have recently been carried out. In the present study, a comparative approach was applied to estimate the concentration of chlorophyll-<i>a</i> at Paldang Dam, South Korea using hyperspectral data. We developed a framework for estimating chlorophyll-<i>a</i> using dimension reduction methods, such as principal component analysis and partial least squares, and various machine learning algorithms. We analyzed hyperspectral data collected during a field survey to locate peaks in the chlorophyll-<i>a</i> spectrum. The framework that used support vector regression achieved the highest R² of 0.99, a mean square error (MSE) of 1.299 μg/cm³, and showed a small discrepancy between observed and real values relative to other frameworks. These findings suggest that by combining hyperspectral data with dimension reduction and a machine learning algorithm, it is possible to provide an accurate estimation of chlorophyll-<i>a</i>. Using this, chlorophyll-<i>a</i> can be obtained in real time through hyperspectral sensor data input from drones or unmanned aerial vehicles using the learned machine learning algorithm.