The aim of this study was to model sea lice levels and the effect on reproduction by a stochastic simulation model and to evaluate the uncertainty of lice estimates based upon counts. Two empirical data sets were examined to parameterize the models. An overall fit of the data to the Poisson distribution was found and thus was used as the base of the stochastic models. In the model, salmon lice reproduction is not linear with the number of adult females and at low lice loads a smaller proportion of the adult female lice will reproduce. Depending on the variance structure, it was estimated that between 40% and 60% of the adult female lice will reproduce at an abundance of 0.5 adult females per fish. Lice counts, especially when examining few fish at low lice loads, are uncertain and at a true abundance of 0.1 one may count between 0 and 5 lice when examining 10 fish. Understanding the dynamics of sea lice reproduction is a key factor in the development of sustainable control strategies.