Based on the water discharge at Gaochang Hydrological Station (GCHS) in Minjiang River, Beibei Hydrological Station (BBHS) in Jialingjiang River, and Wulong Hydrological Station (WLHS) in Wujiang River from 1956 to 2018, this paper analyzes the trend changes, mutation years, and periodic changes of water discharge at each hydrological station by methods of 5-a sliding average, M-K nonparametric test, cumulative distance level test, and sliding t-test. Furthermore, we investigate the response of water discharge changes to El Niño-Southern Oscillation (ENSO) and East Asian summer winds (EASW) by the method of Morlet wavelet analysis. The results show that there are significant alternating characteristics with wet-dry water discharge at each station. The inter-annual fluctuation of water discharge is relatively moderate and generally shows a decreasing trend, among which the decreasing trend at GCHS is significant. The mutation years of water discharge are 1969 and 1993 at GCHS, 1993 at BBHS, and 1993 and 2004 at WLHS. The water discharge series shows significant periodic variations at an interannual timescale of 2 to 8 years and an interdecadal timescale of 16 to 17 years. The water discharge changes respond to ENSO and EASW from lagging to overtaking with the increasing intensity of human activities, such as the construction of water conservancy projects and soil and water conservation measures. Responses of water discharge to ENSO have periodic variations at an interannual timescale of 2 to 6 years and an interdecadal timescale of 16 to 17 years, and to EASW, and the joint action of ENSO and EASW has periodic variations at an interannual timescale of 2 to 6 years.