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The Oceanographic Research Facilities program manages, under a charter party agreement with selected universities, the operation and maintenance of all oceanographic research vessels owned by ONR for Department of the Navy.

The Littoral Geosciences and Optics program (ONR 322LO) supports basic and applied research for expeditionary warfare, naval special warfare, mine warfare and antisubmarine warfare in shelf, near-shore, estuarine, riverine and riparian environments, with a particular emphasis on robust 4D prediction of environmental characteristics in denied, distant or remote environments.

The Explosive Hazards Defeat (EHD) program invests in basic research, applied research and advanced technology development to support development of new capabilities in on-the-move standoff detection and neutralization of explosive hazards.

The Marine Mammals and Biology (MMB) program supports basic and applied research and technology development related to understanding the effects of sound on marine mammals, including physiological, behavioral, ecological and population-level effects.

The Office of Naval Research's Marine Meteorology and Space program sponsors innovative basic and applied research in the broad thrust areas of atmospheric prediction, atmospheric effects, air-sea interaction and marine boundary layer processes and space environment.

The Office of Naval Research's Maritime Sensing program conducts multidisciplinary science and technology, research and development of acoustic and non-acoustic sensors and transduction systems as a means to provide next-generation sensing technologies for the Navy’s tactical surveillance and undersea warfare missions.

ONR's Ocean, Atmosphere and Space Research Division participates in the National Oceanographic Partnership Program.

The Office of Naval Research's Ocean Acoustics program supports basic research that addresses fundamental understandings of the physics relating to underwater sound.

The Ocean Engineering and Marine Systems program seeks to provide a knowledge framework for advanced engineering methodologies and to accelerate the transition of basic research developments into advanced marine platform systems with applications to unmanned surveillance and monitoring systems for the naval forces and at-sea experimental capabilities for the ocean sciences community.

The Office of Naval Research's Power Electronics & Electromagnetism, Adaptive & Machinery Controls and Advanced Machinery Systems program supports the Navy’s interest in advanced naval power and energy systems science and technology, and autonomous technology.