UNESCO-IHE offers 18-month Master of Science (MSc) programmes that start every year in October.

The first year of the programme consists of taught modules. This is followed by six-month research period resulting in a thesis.

Each module is taught over a three-week period, is structured around a central theme and has a certain number of credit points. UNESCO-IHE uses the European Credit Transfer System (ECTS), in which each credit point is equivalent to 28 study load hours. The UNESCO-IHE Master of Science programme consists of 106 credit points in total.

When the participant has successfully completed the taught modules, he or she will enter an individual research programme for a six-month period, under the guidance of a supervisor. The study is completed with the MSc thesis and a public presentation of its results, which are judged by an examination committee.