One of the factors with the most significant impact due to pollution caused by mining activities is water. Surface water resources are limited, and in many cases, they are the primary water source for consumption; thus, its quality is a fundamental subject of study. The traditional way of studying water quality is to measure parameters and compare the results with tables of values established in the regulations. The quality of drinking water is characterized and controlled. However, this traditional comparison method may be subjective and insufficient to classify water quality as safe. Therefore, it is necessary to develop and complement the conventional monitoring, linking physicochemical analysis with remote perception. The different variables analyzed can be integrated and result in much more complete water quality indices, achieving the evolution of the monitoring programs of the water quality of the surface bodies. This research combines remote sensing with traditional monitoring to obtain a more robust and affordable indicator, resulting in a study of the central water bodies of Milluni. The main finding—the alarming contamination in the Milluni Chico and Milluni Grande lagoons—provides more accurate information to decision-makers to improve water management in Bolivia.