Development and conservation of valley ecosystems has been an important issue for a long time, with respect to extensive, interdisciplinary research problems, offered ecosystem services and wide public interest. It has been as yet controversial, which indicators would describe the achievement of particular environmental status by those ecosystems, since they tend to be rather complex, showing fragile equilibrium and high vulnerability. With the use of hydrological modelling and proper criteria we demonstrated possibilities to balance well the concern for managers to control features regarding ecosystem health. It was evident during different hydroperiods, that ground water inflow conditions, influenced by investments into hydraulic structures functioning, arise as driving factor for environmental and ecological disturbance.