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Karst terrains are generally regarded as a fragile and vulnerable environment. China’s karst is mainly developed in pre-Triassic, old-phase, hard, compact carbonate rock. The lack of soil cover in bare karst land can enhance desertification. Its underground drainage system can aggravate both drought and flooding problems; the interconnected surface and subsurface conditions allow for easy contamination by pollutants. Moreover, karst terrains quite often suffer from a series of engineering problems, such as water infiltrating into mines or transportation tunnels, leakage from reservoirs, and failure of building foundations. As resources and energy exploitation intensified in recent years, karst areas in Southwest China faced some severe geo environmental problems. In order to find out how the problems action and evolution in recent years, field and laboratory investigations were conducted in Guangxi autonomous region, Guizhou, Yunnan, Guangdong, Hunan, Hubei provinces, and Chongqing municipality. About 100 experts from the Provincial Geological Survey and graduate students took part in this project. Several symposiums were held during those 3 years. Besides the in situ survey, data were collected from hydrogeological survey results since 2000 when the new round of land resources investigation began. After analyzing these data, rock desertification, drought and flooding, and contamination and engineering geological environmental problems were considered the most prevalent problems in karst areas in Southwestern China. The status of each problem is elaborated upon in this paper and should be considered for future sustainable development.