Sea lice are a persistent problem for farmed and wild salmonid populations. Control can be achieved through the use of veterinary medicines. A model was developed to describe the patterns of sea lice infection on salmon farms in Scotland and to predict the likely effect of various treatment strategies. This model takes into account development rates and mortality using compartments representing life history stages and external infection pressure. The national sea lice infection pattern was described using parameters representing stage survival, background infection levels and egg viability rates. The patterns observed across farms varied greatly and the model gave broad agreement to observed trends with different parameters being required in the model for sites using hydrogen peroxide and cypermethrin treatments. The parameter estimates suggest that the background infection pressure on sites where cypermethrin was administered was higher than for those using hydrogen peroxide. Both models had comparable magnitudes of sensitivity with survival from one stage to another being the most sensitive parameter, followed by feedback rates at which gravid females produce eggs, with background infection levels the least sensitive. The effect of different cypermethrin treatment strategies was assessed using the model. Increasing treatments in a production cycle gave more effective control. However, the model showed that timing of treatments is most important if sea lice are to be effectively controlled.