To maintain the ecosystem health and guarantee the social-economic water demand in the Dongjiang river basin, proper management of the water resources is essential. This research introduced the Morlet Wavelet analyses method to investigate the patterns of the past 45 years runoff times series of the main gauges in the Dongjiang River. The general trend and the changing characteristics in both time domain and frequency domain at different scales were revealed. The results were verified by the real part of the Wavelet coefficient and the Wavelet variance. The study discovered that the runoff in the basin exhibited multi-scales of main circle, synchronization and declining. The results could provide valuable information for the management of the water resources and ecosystem of the Dongjiang River.