Anthropogenic waterways and canal systems have been part of the cultural and natural landscape for thousands for years. As of the late 20th century, more than 63,000-km of canals exist worldwide as transport routes for navigation, many with barriers (e.g., locks, dams) that fragment the system and decrease connectivity. Fragmentation alone can have negative implications for freshwater biodiversity; by isolating populations and communities, other human-mediated disturbances associated with canals like poor water quality and invasive species can exacerbate these negative effects. As such, the capacity of these interconnected freshwater systems to support biodiversity is continuously degrading at a global level. One critical, highly complex issue that unites canals worldwide is the challenge of governing these systems in a holistic, unified way to both protect biodiversity and preserve historical elements. Managing historic canals involves multiple objectives across many agencies and stakeholders, often with different or conflicting objectives. Here, we use the Rideau Canal, a UNESCO World Heritage Site and National Historic Site of Canada, as a case study to demonstrate the importance of considering canals as social-ecological systems for effective and efficient governance. Historic canals are integrated systems of both humans (social) and the environment (ecological), linked by mutual feedbacks and coevolution, and must be managed as such to achieve conservation goals while maintaining commemorative integrity. We discuss the history of the Rideau Canal and its current governance, biodiversity in the waterway, different threats and issues (user conflicts, aquatic pollution, shoreline development, water management, species at risk, and invasive species), and conclude by outlining ways to address the challenges of managing it as a coupled social-ecological system. We present different research needs and opportunities that would enable better management, though above all, we propose a shift from the current governance structure – which at best can be considered “patchwork” – to a coordinated, multi-scalar and multi-stakeholder governance regime such that the Rideau Canal can be maintained for its historical integrity without compromising biodiversity conservation. Given that canals are now pervasive worldwide, this article is not only topical to the Rideau Canal, but also to other waterways in Canada and beyond.