Reservoir characterization is necessary for making reliable models to have future reservoir performances. Since an aquifer typically has positive influences on oil production, its characterization has rarely been regarded as a critical issue. However, in channel oil reservoirs, an aquifer amplifies uncertainty of permeability estimations and has its own uncertainty due to limited information without any direct measurement. Although there have been some researches on channel oil reservoirs using discrete cosine transformation, we cannot characterize reliably an aquifer using discrete cosine transformation alone. Thus, we need additional schemes to manage increased uncertainty by an aquifer and to estimate the aquifer itself. In this study, ensemble Kalman filter with the combination of preservation of facies ratio and discrete cosine transformation is proposed for channel reservoirs with an aquifer. By the proposed method, we confirm that discrete cosine transformation and preservation of facies ratio contribute to preservation of overall channel properties and fine-tuning of the channel in the ensemble Kalman filter algorithm, respectively. Consequently, the proposed method gives us stable characterization performances on oil and water productions, permeability distribution, and aquifer strengths for a reasonable decision. Keywords Ensemble Kalman filter, discrete cosine transformation, preservation of facies ratio, channel oil reservoirs with an aquifer, aquifer characterization