Karst aquifers are prominent sources of water worldwide; they store large amounts of water and are known for their beautiful springs. However, extensive groundwater development and climate variation has resulted in a decline in the flow of most karst springs; some have even dried up. In order to obtain a better understanding of the factors contributing to this development, this study introduced grey system models, which quantified spring flow, taking Jinci Springs (China), which dried up in May 1994, as an example. Based on the characteristics of Jinci Springs, spring flow was divided into two stages: first (1954–1960), when the spring flow was affected only by climate variation; and second (1961–1994), when the flow was impacted by both climate variation and anthropogenic activities. The results showed that Jinci Springs flow had a strong relationship with precipitation occurring one year and three years earlier in the first stage. Subsequently, a grey system GM (1,3) model with one-year and three-year lags was set up for the first stage. By using the GM (1,3) model, we simulated the spring flow in the second stage under effects of climate variation only. By subtracting the observed spring flow from the simulated flow, we obtained the contribution of anthropogenic activities to Jinci Springs’ cessation. The contribution of anthropogenic activities and climate variation to the decline was 1.46 m3/s and 0.62 m3/s, respectively. Finally, each human activity that caused the decline was estimated. The methods devised herein can be used to describe karst hydrological processes that are under the effects of anthropogenic activities and climate variation.