As a consequence of climate changes the extreme hydrological phenomena occures, in terms of spatial and temporal variability. In such conditions – of more frequent and extreme high water regimes and reduction of low water – the water storage reservoirs should be used for active flood protection as well as for improving the low water regimes. The possibilities for better flood control in the multipurpose water resources system, including the water storage reservoirs, are analyzed in the paper. Case study described in the paper refers to the Trebišnjica River Hydrosystem (Herzegovina). As a part of the improvement of management process a mathematical simulation model was developed. Model proposes the most favorable operational rules for operation with water gates at the bottom outlet and spillways of the dam, according to the criterion of achieving the best transformation of the flood wave. The main goal is the best possible protection of the Trebinje Town from destructive influence of the flood waves.