Indigenous rights, knowledge, and value systems are linked inextricably to the lands, waters, and non-human beings that form the environments of Indigenous Peoples. Across the globe, the rights of Indigenous peoples are being formally recognized and as a result, efforts are being made to include Indigenous Knowledge and value systems in environmental policy and decision making. Scientists and decision makers must not only recognize this reality, but also operationalize these efforts through meaningful changes to create space for the inclusion of Indigenous Knowledge, Indigenous values, and sovereignty within the current methods for scientific enquiry and the development of environmental policies. Professionals in the environmental field have a responsibility to ensure that their work has a positive impact on Indigenous Peoples and their environments. In this study, we explore the concept of consultation and informed consent through the lens of the development of environmental policy and decision making. We will discuss these concepts in the context of ecological risk assessment related to a case study focused on contaminated sediment in a harbor within the Great Lakes. We will demonstrate a process that deconstructs the current protocols for risk assessments at sites with localized pollutants in sediment and rebuilds them with elements that recognize both Western and Indigenous knowledge systems. This process includes collaborative fieldwork, relationship building, and informal and formal interviews with participants and community members. By utilizing such approaches, we were able to develop a risk assessment framework that recognizes the sovereignty of Indigenous peoples and promotes effective Nation-to-Nation decision making.