Abstract: Correct discriminating the properties of infillings (water or mud) in karst water-bearing media is one of the main “bottle necks” for effective exploration and development of karst water. Both mud and water media are reflected as low resistivity characteristics. So, it is difficult to distinguish whether the water-bearing medium is the water one or the mud one, which often leads to failure in drilling wells. Based on the groundwater geophysical exploration in the karst area in recent years, it is found that it is feasible to identify the water-bearing media with the polarization difference of the water and mud. The basic principle and the field test results with three geophysical methods, the nuclear magnetic resonance method, the induced polarization method, and the spectrum induced polarization method, to identify the water-bearing media filled with water or mud are discussed respectively in the article. If karst aquifer medium is filled with water, there will be a nuclear magnetic resonance (NMR) signals, and a high time-constant value features both tested by induced polarization method and by spectrum induced polarization method. If karst aquifer medium is filled with mud, there is no NMR signal response, and a low time-constant value features both tested by induced polarization method and by spectrum induced polarization method. The above-mentioned conclusions are verified by several cases in different types of media.