The work of the Pyhäjärvi Institute is based on the purpose that was described in the deed of foundation at the time of registration in 1989:
The institute’s mission is to enhance and develop education and research and to carry out other development work concerning the food industry and the environment.
Areas of expertise include the food industry and the upkeep of water bodies, in particular water conservation and restoration. The aim is to sustainably secure competitiveness of food production in the Satakunta region, to improve the condition of the water bodies, to increase knowledge and to practically apply that knowledge to work on water restoration.

The Pyhäjärvi Institute Foundation is administered by a board of 11 members representing participants from local municipalities, local companies and the University of Turku. The board’s term runs from 2017–2019. The executive manager, nominated by the board, is responsible for leading operations. The Board will approve how the work is carried out in conjunction with the operating plan and operating costs, and will monitor fulfilment of the aims. The board convenes two to three times a year.

Implementation of the Pyhäjärvi Restoration Programme is directed by a delegation that convenes twice a year and an executive group that convenes more frequently. Legally, the institute’s board is also responsible for decision-making in the Restoration Programme.
In addition to the executive director, the Institute has eight permanent employees and various temporary employees working on different projects. In 2012 the Institute recorded between 17-19 man-years. In general, the final number depends on funding of the schemes and development of the service.

The Pyhäjärvi Institute is located in Eura.