In the spacious inundation area on the left bank of the lower course of the Sava River in Serbia, there is an abandoned meander Special Nature Reserve, “Obedska bara”, which represents a very important floodplain in this part of Europe. This area is characterized by an exceptional wealth of biodiversity with a significant presence of rare and endangered species of national and international importance. Hydrological conditions in the mentioned area were analyzed from the aspect of surface water movement in nature and conditions altered by human factors (after the construction of the road network, canals, etc.). The movement of surface water, i.e., the filling and emptying of the investigated area, parallel to the water level of the Sava River, is shown using a digital terrain model. Our simulation of the change in surface water level within the studied area included the display of underwater areas, both with the formation of a flood wave (i.e., increasing water level of the Sava) and with the outflow of water from the pond when the water level in the Sava was reduced in both scenarios (natural and conditions altered by human factors). GIS and terrain digitalization were used for geospatial and hydrological analyses and, based on this, maps that display endangered areas could be made. The obtained results show that the largest human impact was recorded at the water level of the Sava River 74 m above sea level. The aforementioned water regime changes were shown to negatively affect dominant vegetation, such as pedunculate oak and ash.