The National Water Quality program aims to protect and improve the quality of water resources throughout the United States and its territories, particularly in agriculturally managed watersheds.The program hopes to bring scientists and educators into effective partnerships with federal programs to address water quality issues.

The CPPM program addresses high priority issues related to pests (including insects, nematodes, pathogens, and weeds) and their management using Integrated Pest Management approaches at the state, regional and national levels.

The Sustainable Bioenergy challenge area focuses on the societal challenge to secure America's energy future. The challenge hopes to implement regional systems that materially deliver liquid transportation biofuels and reduce national dependence on foreign oil while also producing biopower and biobased products. 

The Education and Literacy initiative is dedicated to developing the next generation of research, education, and extension professionals in the food and agricultural sciences. 

The Food Safety challenge area focuses on the societal challenge of ensuring a safe and nutritious food supply while maintaining American agriculture competitiveness.

This program funds research attempting to understand the interaction between climate variability and agricultural production systems to develop the plants, animals and management systems that will be robust and productive under changing environmental conditions while  providing the important ecosystem services needed from these lands. 

The Water for Food Production Systems challenge seeks multidisciplinary systems approaches, which integrate new technologies and strategic management that solve water availability and quality challenges in food production systems.

The Agriculture and Food Research Initiative is one of the main competitive grants programs for the agricultural sciences. It awards grants in several research areas including improving food production efficiency, mitigating climate change impacts, addressing water availability issues and food safety and security.

SAEM aims to enable sustainable buildings and other structures that can be continuously occupied and/or operated during the structure’s useful life. The SAEM program supports fundamental research for advancing knowledge and innovation in structural and architectural engineering and materials that promotes a holistic approach to analysis and design, construction, operation, maintenance, retrofit, and repair of structures.

The Decision, Risk and Management Sciences program supports scientific research directed at increasing the understanding and effectiveness of decision making by individuals, groups, organizations, and society.