Groundwater is an essential water resource in the Yarkant River Basin Irrigation District, which is the largest oasis in Xinjiang, China. This study used a novel approach to analyze the relationship between groundwater depth and three driving factors by developing Copula Functions from monthly time series data collected from 16 monitoring wells. More specifically, marginal distribution and joint distribution functions were established, and the conditional probabilities for three data ranges were calculated using both two- and three-dimensional Copula Functions. The developed statistical models showed that groundwater exploitation, runoff, and surface water irrigation significantly affected groundwater depth. The most significant effect on water table declines was associated with groundwater exploitation and lagged 1-month behind the groundwater withdrawals. The amount of runoff and irrigation were both inversely related to water table depth due to groundwater recharge. Frank Copula Functions were found to produce the best fit to the joint distribution of the variables and were used herein, allowing for the establishment of a detailed probability distribution of the change in groundwater depth under the combined effect of multiple controlling factors. The results provided key insights into how irrigation and groundwater withdrawals can be adjusted to effectively manage groundwater resources.