The Waterkeeper Alliance traces its roots to the Hudson River Fishermen’s Association (HRFA), an organization of recreational and commercial fishermen who came together in 1966 to protect the Hudson River, the source of livelihood for many of its members. In 1983, the HRFA hired a full-time Riverkeeper whose job was to patrol the Hudson River to catch polluters, restore fisheries, and lead citizens in enforcing environmental laws. The Hudson Riverkeepers were successful not just in protecting the river from polluters, they were also able to bring these people and organizations to justice and force them to spend money and participate in the rehabilitation of the river they once polluted. The Riverkeeper project of the HRFA has inspired other environmental organizations not just in the US, but all over the globe to create similar programs in their respective areas in order to protect the rivers, lakes, and other bodies of water in their area. The increase in the number of waterkeeper programs was rapid and so in 1999, the Waterkeeper Alliance was formed to help support these programs.

The Waterkeeper Alliance promotes the use of the Waterkeeper model to organizations that wish to start their own grassroots water preservation programs in their area. The organization believes that uniting all these different organizations and programs gives them a stronger voice when it comes to pushing for reforms in public policy and environmental laws, as well as in apprehending those who violate them. They provide a wide range of support services for individual Waterkeeper programs and connect different programs to each other, making them much more formidable and more difficult to ignore. The organization also provides each Waterkeeper program with the expertise it needs in different areas such as strategic planning, law, science, communications and other areas that would help them strengthen their programs.