Altered rivers and managed flows are a hallmark of civilization and dams are a principal agent of alteration. Peak dam construction occurred at the turn of the last century in Western countries, and many of the largest dams are reaching the end of their service life. As a result, dam operators are increasingly facing a complex renewal/removal decision‐making process in a large part because the economic and social values of dams have changed. The Mactaquac Hydroelectric Generating Station (New Brunswick, Canada), operated by NB Power Corporation (NB Power), is Canada's 25th largest dam and it is reaching the end of its service life. A decision is required for the dam's future state and three options were originally proposed: renew, rebuild, or remove. An overarching science framework was developed with NB Power to inform and support decision‐making for the dam's decision process and an impending Environmental Impact Assessment. The framework guides research and monitoring for dam renewal/removal using science‐based solutions that aim to minimize impacts on the aquatic environment while supporting an efficient and cost‐effective decision‐making process. The framework has five components: (a) establish long‐term baselines of environmental conditions; (b) develop normal ranges describing the river's natural variability; (c) integrated physical and biological modelling; (d) assess the specific and cumulative state of fish passage; and (e) create and sustain a user‐friendly geospatial data management system. In this paper we present a case study that implements the science framework (Part 1) through the Mactaquac Aquatic Ecosystem Study (MAES) with a view to revisit and assess its final impact post‐project completion (Part 2).