In February 2014, the Dynamics and Properties of Marine Systems (DPMS) Theme of the Marine Alliance for Science and Technology for Scotland (MASTS) organised a case study workshop on the Loch Linnhe and Firth of Lorn (LL&FL) system. Loch Linnhe is one of the largest sea lochs on the west coast of Scotland, and the Firth of Lorn provides a connection to the open ocean. During the workshop, a review of the current knowledge of LL&FL was undertaken in three subject areas: the physical environment, the aquatic ecosystem and the management and use. This review also identified a number of knowledge gaps and potential collaborations to address these. This report provides an overview of these discussions. A more comprehensive, scientific review of our knowledge of the LL&FL system will be published in the near future.