Cave systems are important tools for inversion of rock desertification. However, the complexity of the climate system, the long-term nature of cave sediment accumulation and the spatial and temporal heterogeneity of karst geologic processes allow the original signals to be altered during transmission. In this work, the isotopic values and environmental parameters of atmospheric precipitation, plant water, soil water, cave drip water and underground river outflow water in the Guizhou karst cave system are monitored in situ on a monthly scale, and the processes of water migration and change are explored in detail. The results showed that precipitation has a significant regulatory effect on the physicochemical properties of the cave microenvironment, and cave drip water exhibits a Ca2+center dot Mg2+-HCO3-hydrochemical type. Atmospheric precipitation is the main water source in the study area, except for plant water isotopes, the remaining water bodies are characterized by seasonal changes. The lag times of the water bodies in the cave system significantly differ during the transmission process, ranging from 2 d to 1 year, which is closely related to the mechanism of water accumulation and release in typical karst landscape areas. The spatial and temporal distributions of water vapor sources, as well as seasonal variations in temperature and precipitation, significantly influence the isotopic changes in water bodies in the study area. Overall, this study provides a systematic study on the migration and transformation process of water bodies in Guizhou karst caves, which provides a new approach and perspective for an improved understanding of hydrological processes and climate change in karst areas.