HOT was founded to understand the processes controlling the fluxes of carbon and associated bioelements in the ocean and to document changes in the physical structure of the water column. To achieve this, the HOT program has several specific goals:
:1. Quantify temporal (seasonal to decadal) changes in reservoirs and fluxes of carbon and associated bioelements (nitrogen, oxygen, phosphorus, and silicon).
:2. Identify processes controlling air-sea carbon exchange, rates of carbon transformation through the planktonic food web, and fluxes of carbon into the ocean.
:3. Form a multi-decadal baseline based on the gathered data that will allow researchers to decipher natural and anthropogenic influences on the NPSG ecosystem.
:4. Provide scientific and logistical support to other scientific programs that benefit from the research and services performed by the HOT program. This includes projects implementing, testing, and validating new methodologies, models, and transformative ocean sampling technologies.
The dissolved inorganic carbon data set that has been accumulated over the course of the HOT program shows the increase of carbon dioxide in the surface waters of the Pacific and subsequent acidification of the ocean. The data collected by these cruises are available online.
The 200th cruise of the HOT program  was in 2008. HOT recently celebrated its 25th year in operation, with the 250th research cruise occurring in March 2013.