The long-term runoff variability is identified to consist of the selected large rivers with long-term data series in the Danube River Basin. The rivers were selected in different regions of the Danube River Basin and have a large basin area (Danube: Bratislava gauge with 131,338 km ; Tisza: Senta with 141,715 km ; and Sava: Sremska Mitrovica with 87,966 km ). We worked with the station Danube: Reni in the delta as well. A spectral analysis was used to identify the long-term variability of three different types of time series: (1) Average annual discharge time series, (2) Minimum annual discharge time series and (3) Maximum annual discharge time series. The results of the study can be used in a long-term forecast of the runoff regime in the future.