Research within MASTS is organised under three broad research themes:

1. Dynamics and properties of marine systems: This theme embraces the fundamental physical attributes and dynamics of marine systems. It also includes technological developments that allow improved interpretation of marine systems.
2. Productive seas: This is a key area of MASTS activity with major scientific challenges encompassing the balance of exploitation against the resilience and capacity of natural systems to supply resources against a backdrop of increasing demand and climate change.
3. Marine biodiversity, function and services: The link between the diversity, distribution in space and time, and resilience of marine organisms is central to this theme, as well as the role of marine biodiversity in supporting ecosystem function and services.

These Research Themes are the largest and most inclusive groupings which reflect the Scottish Marine strategy and Scottish Government objectives in promoting clean, healthy, diverse and productive seas. 

Underneath each Theme, there are groupings called Research Forums, which are intended to be outward looking and to include all MASTS members who have an interest in those areas. Forums are the main delivery mechanism for MASTS science. Although Forums are associated with a Research Theme, they may cut across other Themes. Forums can be established to address specific areas of research as they emerge but to receive funding and other MASTS support, they must be approved by the MASTS Executive Committee and operate within prescribed guidelines. Each Forum is led by a Convenor and has an annual networking budget.