“One of the finest natural areas yet discovered” was the way John McTaggart, a young British engineer, described Hamilton Harbour in 1827. By 1969, it was described in the Canadian Parliament as a “stinking rotten quagmire of filth and poisonous waste.” The “industrial heart of Canada” and “Steel City” are other descriptions that defined Hamilton and its harbour, setting the background for the image shared by most local and Canadian citizens. This image has persisted well past the turn of the 21st Century, even as things change.Hamilton Harbour is a special place for research precisely because it has absorbed and succumbed to urbanization and industrialization. It is a special place because as a community, citizens, industry, scientists and governments come together to reinvent this Harbour and remediate its ecosystem. The remediation process is not complete at the time of this publication, but it is within sight. Telling the story of progress to date is overdue; hence this special issue of the Journal of the Aquatic Ecosystem Health and Management Society (AEHMS). The science in Hamilton Harbour could not take place without the support of the community, and the remediation of this Harbour could not take place without the science to direct actions. There are 19 varied partner agencies in the Bay Area Implementation Team that directs and leads the remedial actions: ArcelorMittal DofascoBay Area Restoration CouncilCity of BurlingtonCity of HamiltonConservation HaltonEnvironment and Climate Change CanadaFisheries and Oceans CanadaGreen VentureHamilton Conservation AuthorityHamilton Halton Home Builders’ AssociationHamilton Harbour RAP OfficeHamilton Port AuthorityHamilton Waterfront TrustMcMaster UniversityOntario Ministry of the Environment and Climate ChangeOntario Ministry of Natural Resources and ForestryRegional Municipality of HaltonRoyal Botanical GardensU.S. Steel CanadaThe Hamilton Harbour Remedial Action Plan is a model for community, government and scientists collaborating to one end: the eventual delisting of the Harbour from the designation, under the Great Lakes Water Quality Agreement, as an Area of Concern.This special issue reports on some of the ongoing science under the topics: Physical-chemical regime, toxic contaminant dynamics, and biotic community dynamics. The Hamilton Harbour community knows these topics as water quality, toxics, and fish and wildlife. Major projects are underway to remediate the Cootes Paradise Marsh, clean up a toxic blob known as Randle Reef, and upgrade wastewater treatment systems. These are not insignificant undertakings. Randle Reef is the largest sediment remediation project on the Canadian side of the Great Lakes and the most contaminated site of its kind in Canada. Upgrades to our wastewater treatment plants will push their function to the highest level practically achievable in tertiary treatment. Cootes Paradise Marsh restoration is one of the most notable and innovative freshwater marsh restorations of its kind in North America. In the end, close to two billion dollars will have been invested in remedial actions, science, and monitoring to remediate Hamilton Harbour.It is important to recognize that this collaborative effort would not have occurred without the work of several key individuals. We wish to acknowledge the role of the following individuals who have led, but are now retired from, this remediation effort: Anne Redish, former Chair of the Hamilton Harbour Stakeholder Forum; Dr. Keith Rodgers, first RAP Coordinator and leader of the original science writing team; Murray Charlton, former Head of the Hamilton Harbour Technical Team; Victor Cairns, former Chair of Fish and Wildlife Restoration; Dr. Peter Rice and Len Simser, leaders of the Cootes Paradise Restoration; Ken Hall, former Executive Director of the Bay Area Restoration Council; and Kathy Trotter, former Administrative Assistant for the Hamilton Harbour Remedial Action Plan. Finally, a special acknowledgement to the late Dr. Brian McCarry, whose understanding of the issues and ability to explain them to anyone are greatly missed. These people set an example for the many scientists and community workers who continue and expand their efforts.Thanks are also due to to Dr. Mohi Munawar and the staff of the AEHMS who were instrumental in organizing this special issue.