There is a vast body of knowledge that eutrophication of lakes may cause algal blooms. Among lakes, shallow lakes are peculiar systems in that they typically can be in one of two contrasting (equilibrium) states that are self-stabilizing: a ‘clear’ state with submerged macrophytes or a ‘turbid’ state dominated by phytoplankton. Eutrophication may cause a switch from the clear to the turbid state, if the P loading exceeds a critical value. The ecological processes governing this switch are covered by the ecosystem model PCLake, a dynamic model of nutrient cycling and the biota in shallow lakes. Here we present an extensive analysis of the model, using a three-step procedure. (1) A sensitivity analysis revealed the key parameters for the model output. (2) These parameters were calibrated on the combined data on total phosphorus, chlorophyll-a, macrophytes cover and Secchi depth in over 40 lakes. This was done by a Bayesian procedure, giving a weight to each parameter setting based on its likelihood. (3) These weights were used for an uncertainty analysis, applied to the switchpoints (critical phosphorus loading levels) calculated by the model. The model was most sensitive to changes in water depth, P and N loading, retention time and lake size as external input factors, and to zooplankton growth rate, settling rates and maximum growth rates of phytoplankton and macrophytes as process parameters. The results for the ‘best run’ showed an acceptable agreement between model and data and classified nearly all lakes to which the model was applied correctly as either ‘clear’ (macrophyte-dominated) or ‘turbid’ (phytoplankton-dominated). The critical loading levels for a standard lake showed about a factor two uncertainty due to the variation in the posterior parameter distribution. This study calculates in one coherent analysis uncertainties in critical phosphorus loading, a parameter that is of great importance to water quality managers.