The construction of barrier structures on the watercourses causes hydro morphological changes in the river system. Water reservoirs due to the retention of high waters change the drainage regime as well as the dynamics of sediment transport. Sediments are as a function of hydrodynamic conditions deposited and eroded in the area of the reservoir and cause morphological changes in the reservoir batimetry. Morphological changes - especially the accumulation of sediments - have many effects on the implementation of dedicated uses on reservoirs. The paper presents the theoretical foundations of the management on multi-purpose reservoirs, sediment transport and a description of methods for analysis of morphological changes in reservoirs. The practical part of the thesis was to analyse a multipurpose shallow reservoir Pernica I based on of existing hydrological, topographical and sediment characteristics. Firstly a static analysis of changes in volume of the reservoir using GIS software tools was made and secondly a dynamic analysis of the changing morphology of the reservoir bathimetry with using a two-dimensional hydraulic mathematical model of morphological changes. Based on the calibrated morphological model a simulation of morphological changes untill 2020 and their impact on the primary purpose of reservoir (floodwater retention) was simulated.