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” (FMA), regulator defined “Disease Management Areas” (DMA), and “Fish Health Management Reporting areas” (FHMRA). FMAs balance many operational requirements, while DMAs’ sole purpose is to limit 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 (ISA) 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 one year 06/2013-06/2014. 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 two. 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 management within water bodies at the scale of 50-100 km would be most effective.