We report an application of the Science and Policy Integration for Coastal System Assessment (SPICOSA) Systems Approach Framework (SAF) to Loch Fyne, a fjord in western Scotland. The issue was the potential for conflict between shellfish aquaculture and recreational use for yachting. This was investigated by building an ecological-economic model to simulate: (1) release of modern anti-fouling compounds by recreational boats; (2) dilution of these in the upper layers of the loch by exchange with the sea; (3) their effects on photosynthesis by phytoplankton; (4) the role of phytoplankton (along with non-algal particulate matter) in providing food for mussels; (5) the growth of seeded mussels to harvest, determining (6) the cash input to farms, offset by their costs and allowing (7) the farm revenue to be compared with that from marinas used to berth the yachts. It was concluded from simulations that no noticeable effect on mussel harvest would occur (from this route) for any likely number of yachts berthed in the loch. The application took place in consultation with a local environmental forum and a small reference group of public officials; we reflect on it in the context of a 3-component schema for the science-policy interface and changes in the culture of UK science.