In this paper an analysis of the lowland reservoir operation in atypical conditions is presented. The chosen study object is the Stare Miasto reservoir in the Powa river (Poland), which has been in operation since 2006. It is a two-stage reservoir, consisting of an upper sedimentation part and a lower main reservoir. The upper part is separated from the main part by an internal dam with a sluice gate. Such a construction enabled better control of sediment deposits and their removal. The atypical conditions were caused by flood wave propagation in the Powa river and the reservoir in 2014. In the research, three reservoir bathymetries are analyzed—from 2006, 2013, and 2018. Two-dimensional (2D) hydrodynamic modeling is applied to analyze spatial variability of investigated hydraulic parameters. Such an approach enabled better recognition of the changes observed in the reservoir during 2006–2018. In the research, the spatial distributions of the velocities, the shear stresses, and the stream power are the basis for the analyses and comparisons. The simulations enabled identification of the main elements prone to collapse during flood wave propagation. The presented results and approach may be applied for improvement of reservoir design, with special emphasis on specific structures located in a reservoir basin.