The Joint Program offers Doctor of Philosophy (Ph.D.) and Doctor of Science (Sc.D) degrees; students elect which one to receive. All five disciplines of the program are focused on students attaining a doctoral degree. Students are admitted into the program with an undergraduate degree, though students with advanced training are also encouraged to apply.

Two other degrees are also offered jointly by MIT and WHOI:

Engineers degree, which is offered in oceanographic engineering and designates the basic engineering discipline (such as Electrical Engineer, Ocean Engineer).

Masters degree (S.M.), which is available primarily as an interim degree for doctoral candidates or for those who have met the S.M. degree requirements and leave the program.