The BTC Pipeline crosses several sensitive areas in Georgia, including surface and groundwater bodies. The territory that is crossed by the pipeline is seismically active and there is risk of oil spillage. Any oil spilled from a damaged pipe will quickly mix with the river water. It is planned to construct permanent facilities equipped with five permanent tanks and six block valves on six tributaries of the rivers. Nevertheless, the risk of oil spillage remains dangerous for water ecosystems in these sensitive areas. A specific methodology of bio-indication and remediation of water ecosystems which would be used for emergency response in case of oil spills was tested in these sensitive areas. Laboratory experiments on raw oil show differences in sensitivity for a range of phytoplankton species. It is recommended to use indigenous Cyanobacteria compounds for sensitive areas in the Borjomi region for remediation of oil spills.