This article addresses the problem of pollution in the Lena River caused by gold mining enterprises operating in its upper regions. It highlights the ongoing industrial exploitation of ore and placer gold deposits in five regions within the Siberian and Far Eastern federal districts. The most large-scale development is carried out in the Irkutsk region, Buryatia, and Yakutia. Further intensification of gold mining activities will result in significant negative impacts on the ecosystems of the upper reaches of the Lena River basin. In this context, the potential applications of Sentinel-2 satellite data for assessing the ecological conditions of river systems in Yakutia are being explored. The most common water indices, NDTI, AMWI, and Harma, were used in this study. The indices were applied to analyze the area of the Vitim River mouth, which contains the highest concentration of active gold mining license areas in the basin. Test sites were allocated on the Vitim and Lena rivers, as well as on Lake Okhninskoye for control purposes. Water indices were analyzed using the ArcGIS software package, and statistical data processing was conducted in the MS Excel program. It is revealed that the best results for estimating surface water turbidity in the area of the Vitim River mouth are obtained using the AMWI index. Spatial regularities are demonstrated, and the seasonal dynamics of turbidity in the studied water bodies are analyzed. The proposed methodology using the AMWI index can be applied for operational assessment of the state of water bodies in Yakutia under conditions of active anthropogenic pollution. This can facilitate timely implementation of preventive environmental protection measures.