The variation in Lepeophtheirus salmonis sea lice numbers across 40 Scottish salmon farm sites during 1996 to 2000 was analysed using mean mobile abundance for 3 important 6 mo periods within the production cycle. Using statistical regression techniques, over 20 management and environmental variables suspected to have an effect on controlling lice populations were investigated as potential risk factors. The findings and models developed provide a picture of mobile L. salmonis infestation patterns on Scottish farm sites collectively. The results identified level of treatment, type of treatment, cage volume, current speed, loch flushing time and sea lice levels in the preceding 6 mo period to be key explanatory factors. Factors such as stocking density, site biomass, water temperature and the presence of neighbours, previously cited to be important correlates of sea lice risk from analysis of individual sites over time, were not found to be important. Variation in mobile abundance in the first half of the second year of production could be adequately explained (adjusted R2 between 55 and 72%) by the recorded data, suggesting that there is scope for management to control L. salmonis abundance, though much of the variation remains unexplained.