During his undergraduate studies at Duke University, Dr. Emanuel worked for the United States Geological Survey (USGS) as a Hydrologic Aid, where he collected and processed data from stream and rain gage networks associated with the Environmental Protection Agency's urban stormwater permitting and Federal Emergency Management Agency's floodplain mapping and long-term monitoring programs. After graduating, he joined Trex Company in Raw Materials Procurement and ERP Integration in 1999. In this role, he oversaw the purchase of recyclable plastic for manufacturing and developed a geospatial database for raw materials.

While in graduate school, Dr. Emanuel worked numerous jobs. He was a Graduate Fellow with Blandy Experimental Farm from 2002 to 2006, where he researched carbon cycling and remote sensing. In addition, Dr. Emanuel worked as a Teaching Assistant and Research Assistant at the University of Virginia in the Department of Environmental Sciences (2001-2007). Emanuel completed his postdoctoral work at his alma mater in 2007, Duke University, where he worked at the Center on Global Change.

After completing his postdoctoral work, he joined Appalachian State University's Department of Geology as an Assistant Professor of Geology and Faculty Fellow. While there, he helped co-found the Appalachian Atmospheric Interdisciplinary Research (AppalAIR) Program. Dr. Emanuel worked in the role for three years until he joined North Carolina State University in 2010 as an Assistant Professor of Hydrology. He was promoted to associate professor in 2015 and received tenure as well. In 2016, his teaching and research earned him the title of University Faculty Scholar. He was promoted to professor again in 2020, where he worked until December of 2021. As a professor from 2020 to 2021, Emanuel was selected as a Fellow at the National Humanities Center.

In December 2021, he joined Duke University as an Associate Professor, studying ecohydrology, geosciences, environmental justice, and Indigenous rights. Dr. Emanuel also Co-Chairs the Community Engagement and Environmental Justice program. At the university, he leads researchers studying water and collaborates with Native American Tribes and communities to understand environmental change. His work focuses on community-building through education and relationship-building to amplify the voices of marginalized communities.

His scholarship and dedication to the field have earned Dr. Emanuel numerous awards, including the William C. Friday Fellowship for Human Relations from the Wildacres Leadership Institute, the Steve Wing International Environmental Justice Award from the North Carolina Environmental Justice Network, the Distinguished Service to Indian Education award from the United Tribes of North Carolina, and a nomination for the Governor James E. Holshouser Junior Award for Excellence in Public Service at North Carolina State University, among others.