There are several springs with the large discharge around the Watuputih Karst Hills area that playing a crucial role in supplying water for both domestic and irrigation needs. The springs are located in the fault and fold zones of the Rembang anticlinorium system. This study was designed to determine the characteristics of karst aquifers from one year of monthly spatio-temporal data on discharge parameters and physico-chemical properties (temperature, pH, EC, Ca2+, Mg2+, HCO3–) of the four major springs, namely Brubulan Tahunan, Sumbersemen, Brubulan Pesucen, and Sendang Sayuran. It used statistical calculations to characterize spring discharge and hydrochemical variations, as well as bivariate correlation analysis and flow-duration curve (FDC). The variability index (Iv), variability (V), and spring coefficient of variation parameters (SCVP) classified Brubulan Tahunan and Sumbersemen as springs producing stable, fairly constant discharge with low variations but characterized Brubulan Pesucen as having unstable, varying discharge with moderate variations. The results showed gently sloping hydrograph, low variations in discharge and hydrochemical properties, a relatively prolonged response of discharge and CO2-H2O-CaCO3 interaction to rainfall, and slope changes in the FDC. In other terms, although the springs are controlled by faults and folds, they have diffuse groundwater storage system in the form of densely fractured and porous media. These findings also indicate a less developed interconnected conduit, although Brubulan Pesucen is relatively more developed than Sumbersemen and Brubulan Tahunan. The geological structure and hydraulic gradient formed between the groundwater recharge and discharge areas are proven to control the amount of spring discharge actively.