Complex ecological models are used to predict the consequences of anticipated future changes in climate and nutrient loading for lake water quality. These models may, however, suffer from nonuniqueness in that various sets of model parameter values may yield equally satisfactory representations of the system being modeled, but when applied in future scenarios these sets of values may divert considerably in their simulated outcomes. Compilation of an ensemble of model runs allows us to account for simulation variability arising from model parameter estimates. Thus, we propose a new approach for aquatic ecological models creating a more robust prediction of future water quality. We used our ensemble approach in an application of the widely used PCLake model for Danish shallow Lake Arreskov, which during the past two decades has demonstrated frequent shifts between turbid and clear water states. Despite marked variability, the span of our ensemble runs encapsulated 70–90% of the observed variation in lake water quality. The model exercise demonstrates that future warming and increased nutrient loading lead to lower probability of a clear water, vegetation-rich state and greater likelihood of cyanobacteria dominance. In a 6.0°C warming scenario, for instance, the current nutrient loading of nitrogen and phosphorus must be reduced by about 75% to maintain the present ecological state of Lake Arreskov, but even in a near-future 2.0°C warming scenario, a higher probability of a turbid, cyanobacteria-dominated state is predicted. As managers may wish to determine the probability of achieving a certain ecological state, our proposed ensemble approach facilitates new ways of communicating future stressor impacts.