In this body of work, I examine the process and methodologies applied in scientific research by, on, and with Indigenous communities with an emphasis on diverse ways of knowing in environmental sciences, natural resources, and climate research. Effectively addressing complex social-ecological issues faced within our current and future generations, such as extreme climate variability and environmental justice, will require all relevant sources of knowledge and data, including those held by historically marginalized communities who remain close to the land. Indigenous knowledge systems, informed through generations of careful observation of dynamics of environmental changes are recognized as critical resources for understanding and addressing social-ecological concerns, yet many institutions and researchers have yet to directly address colonial-rooted legacies, including centuries of oppression, ethical violations, and lack of accountability towards the communities who maintain these knowledge systems. My dissertation research draws from theoretical developments in Indigenous methodologies, community-based participatory research, participatory action research, and constructivist grounded theory to enhance our contextual understanding regarding factors inhibiting or supporting diverse knowledge exchange in the sciences. Conceptual contributions include an evidence-based, practitioner-informed analytical framework that can be applied for guiding and evaluating responsible Indigenous community engagement across a wide range of research fields. Using this framework, I provide data findings from the first global systematic review assessing Indigenous community engagement in climate research studies, improving understanding of how research design connects to broader social outcomes for Indigenous communities. In this work I also provide conceptual contributions in the form of a working model for decolonizing community-based science research with Indigenous communities through a cross-disciplinary synthesis of codes of ethics, principles and methodologies for supporting Indigenous sovereignty and self-determination in research. My dissertation explores this model through the values of integrity, respect, humility, and reciprocity to shape intentional commitments and actionable methods that can be applied to raise ethical standards and long-term relational accountability within Indigenous lands and communitiesEmpirical contributions within my dissertation include a case study field-testing and grounding the working model for decolonizing science research through an Indigenous community-based climate study led by youth and elders within two rural agricultural communities in the mountainous central region Borikén (Puerto Rico). This case study highlights innovative participatory methods, resources, and lessons learned to inform processes for aligning cultural and academic institutional protocols for research integrity. My dissertation also explores benefits, barriers, and resources for Indigenous scholars and practitioners engaging Indigenous knowledge systems in their work and research through an in-depth regional case study in the Caribbean. Findings from this research enhance our understanding of how colonial legacies manifest as unique and complex challenges and identifies sources of capacity-building for overcoming these challenges, centering underrepresented narratives from those community members directly impacted by colonial histories. Together, these contributions shape our understanding of how every stage of research process itself, beyond solely the outputs, serve a critical role in decolonizing research and how researchers and institutions can adapt this process towards raising ethical standards in research.