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Human presence, coastal erosion, and tourism activities are increasing the attention to coastal flooding risk. To perform risk assessments, long time series of observed or hindcast wave parameters and tide levels are then necessary. In some cases, only a few years of observation are available, so that observed extreme data are not always representative and reliable. A hindcast system aimed to reconstruct long time series of total tide levels may be of great help to perform robust extreme events analysis and then to protect human life, activities as well as to counteract coastal erosion by means of risk assessments. This work aims to propose a simplified method to hindcast storm surge levels time series in semi-enclosed basins with low computational costs. The method is an extension of a previous work of some of the authors and consists of a mixed approach in which the estimation of storm surge obtained by using the theory of linear dynamic system is corrected by using a statistical method. Both steps are characterized by low computational costs. Nevertheless, the results may be considered reliable enough also in view of the simplicity of the approach. The proposed method has been applied to the Manfredonia case study, a small village located in the Southern Adriatic Italian coast and often prone to coastal flooding events. The comparison of extreme events estimated on the basis of hindcast levels time series is satisfactorily similar to those estimated on the basis of observed tide series.