HErZ is govered by a Scientific Advisory Board (SAB) and a Steering Group (SG), which includes the Administration Office.

The SAB is chaired by the Scientific Advisory Board of DWD, the President of DWD, and the management of the business divisions "Research and Development" (RD), "Climate and Environment", "Weather Forecasting Services" and "Techical Infrastructure and Operations" of DWD. The main tasks of the SAB are the development of the HErZ research programme of the current funding phase and the formation of a commission for the selection and assignment of the external reviewers for the review at the end of a funding phase.

The SG is composed of the main project leaders, the competence area leaders and the Administration Office of HErZ, which consists of the HErZ coordinator and the head of the DWD unit RD "Planning and Coordination" (FEPK). The SG coordinates the cooperation of the competence areas, acts as an interface within the programme and elects the two spokespersons of HErZ if necessary.

The Administration Office in FEPK coordinates, supports and advises the SAB and the SG. It concentrates primarily on cost and investment planning, project controlling, support for the preparation and implementation of the assessments and public relations.