Nestos Delta (north Greece) is a complex ecosystem of high ecological importance, protected by the European Union as a Natura 2000 site. The presence of the habitats 3170* and 91E0*, which are highly connected with water resources availability, impose the continuous monitoring of precipitation in the area, since even minor changes of the precipitation regime could have a significant effect on the habitats’ viability. Aim of this work is to detect significant precipitation changes by analyzing datasets from 5 nearby station for a time period of about 50 years. The results indicate statistically significant decreasing changes mainly at lower altitudes, and increasing at higher.