Turkey's wetlands that represent a very diverse set of ecosystems are subject to considerable risks of biodiversity loss arising from the changes in their hydrology. Maintaining the full spectrum of naturally occurring flows in many rivers is almost impossible in Turkey's economically competing watersheds. Environmental flow assessments may still represent a compromise between water resources development and river ecology maintenance. In the presented study, changes in the water regimes observed in the period 1960–2000 are investigated together with concurrent ecological conditions for over 35 wetlands belonging to different ecological regions. The results, which are presented with indicator-based risk figures to potentially correlate biodiversity loss to decreases in environmental flows in course of time, broadly indicate that substantial risks are estimated in Turkey in terms of environmental flows for wetland systems. Few exceptions appear in the north-east in accordance with the recent climate change predictions indicating precipitation increase trends in the region.