The utilization of Effective Microorganisms (EMs) for lake restoration represents a sustainable approach to enhancing water quality and rebalancing the ecology of aquatic ecosystems. The primary objective of this study was to evaluate the effects of two bioremediation treatment cycles employing EM-enriched biopreparations on water quality in the Siemiatycze lakes. Specifically, this research analyzed various parameters, including dissolved oxygen, transparency, chlorophyll-a, pH, chemical oxygen demand (COD), biochemical oxygen demand (BOD5), total phosphorus, total nitrogen, and suspended matter (SM), across eleven designated sampling locations. Additionally, this study employed remote sensing techniques, leveraging Sentinel-2 satellite imagery and the Maximum Chlorophyll Index (MCI), to detect and quantify algal blooms, with a particular focus on elevated chlorophyll-a concentrations. This comprehensive approach aimed to provide a holistic understanding of the impact of biotechnological reclamation on aquatic ecosystem restoration and sustainability. The study’s findings indicated a significant improvement in water quality in all lakes, with enhanced water clarity and oxygen profiles. Further, remote sensing studies indicated a reduction in algal blooms, particularly those with high chlorophyll-a concentrations. A considerable decrease in water eutrophication intensity was observed due to diminished nutrient concentrations. The improvements in water parameters are likely to enhance the living conditions of aquatic organisms. These results demonstrate the effectiveness of using EM-enriched biopreparations in the bioremediation of lakes, providing a sustainable approach to enhancing water quality and balancing aquatic ecosystems.