With the more frequent human activities, the ecosystem is facing an unprecedented pressure from the human communities. The quantification of the impact from the human activities becomes critical to the ecosystem. Impervious surface area (ISA) is defined as constructed surfaces (roofs, roads, parking lots, and other man-made surfaces) that prevent water from infiltrating into the soil. As a key index of the anthropological change on the Earth surface, ISA is highlighted in the urban remote sensing and urban ecology recently. In this study, we presented two methods to estimate the fraction of ISA on the Earth surface using remote sensing technology. The first one was the Pre-screened and Normalized Multiple Endmember Spectral Mixture Analysis (PNMESMA) whose target is the fractional ISA in a watershed, using satellite images with medium spatial resolution; the other one was Temporal Mixture Analysis (TMA) whose target is the ISA monitoring at national scale, using satellite images with high temporal resolution. Then the impact of the ISA on the water quality and characteristics of discharge in Lake Kasumigaura Basins as a case study was discussed. In addition, other studies were reviewed on the application of ISA in freshwater ecosystem. Further inter-disciplinary study is expected as future work.