Fragmentation (establishment of barriers e.g., hydropower dams, reservoirs for irrigation) is considered one of the greatest threats to conservation of river systems worldwide. In this paper we determine the fragmentation status of central Chilean river networks using two indices, namely Fragmentation Index (FI) and Longest Fragment (LF). These are based on the number of barriers and their placement as well as river length available for fish movement. FI and LF were applied to eight Andean river basins of central Chile in order to assess their natural, current (2018) and future (2050) fragmentation at the doorstep of a hydropower boom. Subsequently, we exemplify the use of these indices to evaluate different placement scenarios of new hydropower dams in order to maximize hydropower use and at the same time minimize impact on fish communities.