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In modern large-scale salmon aquaculture, sites are managed within spatial units. In Scottish waters, several different definitions are used: operator-defined ‘Farm Management Areas’ (FMAs), regulator-defined ‘Disease Management Areas’ (DMAs) and ‘Fish Health Management Reporting areas’ (FHMRAs). FMAs balance many operational requirements, while the sole purpose of DMAs is to limit the spread of disease. FHMRAs are based on historical wild fish monitoring areas. One objective of these units is to monitor and limit the spread of water-borne agents such as infectious salmon anaemia and parasites such as sea lice, which present a perennial economic and ecological challenge. However, unit boundaries are either based on simplified hydrodynamic assumptions, or do not incorporate such information. Their effectiveness for infection control is therefore unclear. We used the latest developments in hydrodynamic modelling to predict population connectivity of sea lice between all current operational salmon aquaculture sites in the complex west coast of Scotland region over 1 yr (June 2013 to June 2014). Aggregating site connectivity matrices by management units, we identified the extent to which units supplied lice to (or received lice from) other units, and their effectiveness for infection control. Total estimated connectivity varied over time by a factor of 2. A general northward movement of simulated larvae was observed. Even the smallest management units reduced external infection by around 75% versus individually managed sites. Larger management units reduced estimated connectivity further. Optimised units derived by applying thresholds to site matrices suggested that management within water bodies at the scale of 50 to 100 km would be most effective.

Temporal variability in sea lice population connectivity and implications for regional management protocols