In this paper, a systematic approach which is able to consider different types of geological uncertainty is presented to model the waterflooding process. The proposed scheme, which is based on control and system theories, enables the experts to apply suitable techniques to optimize the production. By using the developed methodology, a reasonable mapping between defined system inputs and outputs in frequency domain and around a specific operating point is established. In addition, a nominal model for the process as well as a lumped representation for uncertainty effects are provided. Based on the proposed modeling mechanism, reservoir management goals can be pursued in the presence of uncertainty by utilization of complicated control and optimization strategies. The developed algorithm has been simulated on 10th SPE-model#2. Observed results have shown that the introduced methodology is able to effectively model the dynamics of waterflooding process, while taking into account the assumed induced geological uncertainty. (C) 2018 Elsevier Ltd. All rights reserved.