Karst aquifers are highly heterogeneous, and non-stationary systems in terms of hydrodynamic properties. The investigation of the different transport properties and characteristics of a karst aquifer system (KAS) is of great significance for the management and protection of karst aquifers. To investigate the response of discharge (Q), suspended sediment (SS), and temperature (T) to the precipitation (P), we performed correlation, spectral, and wavelet analyses on the hydrologic time series that included mean daily value from 2009/1/1 to 2015/12/31 from the Nandong underground river system (NURS), a large (> 1600 km²) karst-groundwater basin in southern China. The long memory effects can be determined from the autocorrelation functions of the Q, SS and T implied that the NURS has a significant amount of storage. The sharp and narrow cross-correlation function (CCF) peaks and the cross-wavelet transform (XT) power spectrum of the SS vs. P indicated that the response of the SS to P was shorter than that of the Q and T, and also indicated that the weak memory effect and small inertia of the karst systems with regard to SS. The CCF and XT power spectrum indicated that an increase in Q was the main factor triggering the increase in SS, not precipitation, which is contrary to results determined for other karst springs. Furthermore, the XT and cross-wavelet coherence (TC) of T vs. the air temperature (T_a) was used to demonstrate that T_a is not a direct control on the T in the NURS, which can be misinterpreted when using the traditional correlation and spectral analyses.