While modeling water dynamics in dam reservoirs, it is usually assumed that the flow involves the whole water body. It is true for shallow reservoirs (up to several meters of depth) but may be false for deeper ones. The possible presence of a thermocline creates an inactive bottom layer that does not move, causing all the discharge to be carried by the upper strata. This study compares the results of hydrodynamic simulations performed for the whole reservoir to the ones carried out for the upper strata only. The validity of a non-stratified flow approximation is then discussed.