Mineral water from the Changbai Mountain basalt area is China's most important source of drinking water. Mineral water with abundant output and enriched trace elements has driven the rapid development of the local economy. However, the extensive exploitation of mineral water and the neglect of ecological base flows threaten interdependent river ecosystems. In order to ensure the sustainable use of mineral water, it’s necessary to calculate the exploitation and utilization of mineral water according to the ecological base flow. In this study, four hydrological methods were used to analyze the intra-annual and inter-annual ecological base flows, namely the Tennant method, the base flow ratio method, the driest monthly average flow method and the Texas method. The results show that the ecological base flow during the flood season is about 3–4 times that during the non-flood season. Affected by rainfall and runoff, the inter-annual ecological base flow also fluctuated within a small range. This study divides the mineral water exploitation coefficient into five categories and proposes an assessment of the mineral water exploitation potential based on the ecological base flow. It shows that the flow of Baijiang River spring group is the largest, but it’s exploitation potential is normal. Huangni River spring group at weak level for exploitation because of its small flow rate. It’s obvious that river runoff is not the only factor that determines the exploitation coefficient of the spring group. The proportion of ecological base flow and the proportion of river base flow are also important factors.