Based on the measured hyperspectral data and concentration of chlorophyll a, total suspended matter (TSM) and turbidity obtained during June 11 to 13, 2015 in Weishan Lake, empirical models and PSO-SVM model were established to retrieve the three water quality parameters. Meanwhile, the performance of those models was evaluated to determine the models applied to ensemble modeling. The ensemble models containing EW-CM, SPA-CM and BMA were established to retrieve the three water quality parameters by using deterministic ensemble method and probabilistic ensemble method. The deterministic and probabilistic ensemble method was based on the entropy weight method along with pair analysis method and Bayesian averaging method, respectively. Bayesian averaging method was employed to obtain the retrieval uncertainty range of the three water quality parameters by using the single model and the BMA ensemble model, and the retrieval uncertainty range of these models was compared. These results demonstrated that (1) the accuracy of SPA-CM model was better than that of EW-CM model in deterministic ensemble models; (2) the modeling accuracy of BMA probabilistic ensemble model was better than that of SPA-CM and EW-CM model; the verification accuracy of BMA probabilistic ensemble model was similar with that of EW-CM model but slightly lower than that of the SPA-CM model; (3) Probabilistic ensemble modeling could obtain the retrieval uncertainty range of water quality parameters by using the ensemble model and the single model; (4) The deterministic and probabilistic ensemble model associated with the single model information showed a higher modeling and verification accuracy, which could be used to reduce the uncertainty of water quality parameters retrieval compared with single model and promote the retrieval accuracy of water quality parameters in a manner.