Large dams have provided extensive benefits during the past 60 years but have also resulted in ecological and social consequences that were unexpected or were deemed to have a lower societal importance than the design benefits. The management of large dams is still a relatively new scientific issue, compared to the timeframe necessary to detect and understand all the consequences occurring at the watershed scale. This paper summarizes the unforeseen or unanticipated environmental consequences of these projects and potential ramifications to the overall project performance. The value of a central knowledge base and the importance of a system-wide monitoring program to assess pre- and post-implementation conditions and adapt operational rules are presented. Knowledge developed in several basins is reviewed in the context of future strategies for Chile. Chile has a strong economy, looming energy crisis and is faced with balancing the long-term value of a renowned natural landscape with unique ecology and the largest salmon aquaculture industry in the world against the prospect of low cost hydropower to drive other sectors of the economy. This paper outlines the hydroinformatics technologies and scientifically based management approaches that can be applied to this complex issue.